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Krypton in PDB 6eye: Crystal Structure of Murine Neuroglobin Under 150 Bar Krypton

Protein crystallography data

The structure of Crystal Structure of Murine Neuroglobin Under 150 Bar Krypton, PDB code: 6eye was solved by T.Prange, N.Colloc'h, P.Carpentier, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.41 / 1.70
Space group H 3 2
Cell size a, b, c (Å), α, β, γ (°) 87.854, 87.854, 113.210, 90.00, 90.00, 120.00
R / Rfree (%) 19.4 / 25.4

Other elements in 6eye:

The structure of Crystal Structure of Murine Neuroglobin Under 150 Bar Krypton also contains other interesting chemical elements:

Iron (Fe) 1 atom

Krypton Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 17;

Binding sites:

The binding sites of Krypton atom in the Crystal Structure of Murine Neuroglobin Under 150 Bar Krypton (pdb code 6eye). This binding sites where shown within 5.0 Angstroms radius around Krypton atom.
In total 17 binding sites of Krypton where determined in the Crystal Structure of Murine Neuroglobin Under 150 Bar Krypton, PDB code: 6eye:
Jump to Krypton binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Krypton binding site 1 out of 17 in 6eye

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Krypton binding site 1 out of 17 in the Crystal Structure of Murine Neuroglobin Under 150 Bar Krypton


Mono view


Stereo pair view

A full contact list of Krypton with other atoms in the Kr binding site number 1 of Crystal Structure of Murine Neuroglobin Under 150 Bar Krypton within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Kr203

b:32.3
occ:1.00
OG A:SER55 3.4 22.1 1.0
CD2 A:LEU56 3.6 31.0 1.0
N A:ALA29 3.7 18.1 1.0
CD2 A:PHE32 3.7 22.1 1.0
CA A:ALA29 3.7 18.1 1.0
CG A:LEU56 3.8 27.1 1.0
C A:PHE28 3.8 17.8 1.0
CE2 A:PHE32 3.9 22.4 1.0
KR A:KR215 3.9 34.5 0.2
O A:PHE28 3.9 19.3 1.0
O A:PRO52 4.1 25.1 1.0
CD1 A:LEU56 4.1 31.3 1.0
CE2 A:PHE61 4.2 20.6 1.0
CB A:PHE28 4.2 20.9 1.0
CB A:ALA29 4.2 19.7 1.0
CZ A:PHE61 4.4 20.5 1.0
CA A:PHE28 4.6 20.5 1.0
O A:THR25 4.7 23.0 1.0
CB A:SER55 4.7 21.6 1.0
C A:PRO52 4.7 25.2 1.0
CG A:PHE32 4.8 20.8 1.0
CB A:PRO52 4.9 28.9 1.0

Krypton binding site 2 out of 17 in 6eye

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Krypton binding site 2 out of 17 in the Crystal Structure of Murine Neuroglobin Under 150 Bar Krypton


Mono view


Stereo pair view

A full contact list of Krypton with other atoms in the Kr binding site number 2 of Crystal Structure of Murine Neuroglobin Under 150 Bar Krypton within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Kr204

b:37.8
occ:1.00
CG A:LEU136 3.9 38.5 1.0
KR A:KR207 3.9 37.0 0.3
CZ3 A:TRP133 4.0 27.8 1.0
CA A:TYR137 4.0 31.4 1.0
CD2 A:LEU136 4.1 35.8 1.0
CD2 A:LEU113 4.1 23.8 1.0
N A:TYR137 4.2 36.2 1.0
CG2 A:ILE72 4.2 30.9 1.0
CD1 A:TYR137 4.2 32.4 1.0
CG2 A:VAL140 4.2 36.1 1.0
CE3 A:TRP133 4.3 30.8 1.0
CB A:TYR137 4.3 28.8 1.0
CB A:ALA75 4.3 37.3 1.0
C A:LEU136 4.5 35.3 1.0
CG1 A:ILE72 4.6 31.1 1.0
O A:LEU136 4.7 36.2 1.0
CB A:LEU136 4.8 35.9 1.0
CG A:TYR137 4.8 30.7 1.0
CD1 A:LEU136 4.8 42.3 1.0
CB A:ILE72 4.8 28.3 1.0
CB A:VAL140 4.9 34.4 1.0
CA A:ILE72 4.9 28.8 1.0

Krypton binding site 3 out of 17 in 6eye

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Krypton binding site 3 out of 17 in the Crystal Structure of Murine Neuroglobin Under 150 Bar Krypton


Mono view


Stereo pair view

A full contact list of Krypton with other atoms in the Kr binding site number 3 of Crystal Structure of Murine Neuroglobin Under 150 Bar Krypton within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Kr205

b:42.6
occ:0.75
CG1 A:VAL109 3.6 26.5 1.0
CD1 A:ILE72 3.7 31.3 1.0
KR A:KR207 3.7 37.0 0.3
CMC A:HEM202 3.8 39.2 1.0
CG1 A:VAL68 4.1 28.1 1.0
CE1 A:TYR137 4.1 30.3 1.0
CD1 A:LEU27 4.1 25.6 1.0
CD2 A:LEU113 4.2 23.8 1.0
CG1 A:ILE72 4.2 31.1 1.0
CB A:LEU113 4.3 24.4 1.0
CBC A:HEM202 4.4 37.6 1.0
KR A:KR208 4.5 31.0 0.2
CD1 A:TYR137 4.6 32.4 1.0
CG A:LEU113 4.7 27.4 1.0
O A:VAL109 4.8 22.3 1.0
CD1 A:LEU113 4.8 25.6 1.0
CD2 A:LEU27 5.0 24.3 1.0
CZ A:TYR137 5.0 30.8 1.0

Krypton binding site 4 out of 17 in 6eye

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Krypton binding site 4 out of 17 in the Crystal Structure of Murine Neuroglobin Under 150 Bar Krypton


Mono view


Stereo pair view

A full contact list of Krypton with other atoms in the Kr binding site number 4 of Crystal Structure of Murine Neuroglobin Under 150 Bar Krypton within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Kr206

b:39.4
occ:0.40
KR A:KR206 0.0 39.4 0.4
KR A:KR206 1.4 32.5 0.2
CB A:TYR137 3.3 28.8 1.0
CD2 A:LEU114 3.5 32.6 1.0
CG A:LEU114 3.5 34.8 1.0
CG A:TYR137 3.6 30.7 1.0
O A:GLY110 3.6 22.4 1.0
O A:TRP133 3.7 31.1 1.0
CD2 A:LEU113 3.7 23.8 1.0
C A:TRP133 4.0 29.1 1.0
CA A:SER134 4.0 31.3 0.5
CA A:SER134 4.1 30.0 0.5
CD2 A:TYR137 4.1 31.0 1.0
N A:SER134 4.2 29.7 1.0
CG A:LEU113 4.2 27.4 1.0
CD1 A:LEU114 4.2 36.5 1.0
C A:GLY110 4.2 20.6 1.0
CA A:GLY110 4.2 23.7 1.0
CD1 A:TYR137 4.4 32.4 1.0
CB A:LEU113 4.4 24.4 1.0
CB A:TRP133 4.5 29.4 1.0
N A:LEU114 4.6 24.9 1.0
OG A:SER134 4.7 29.7 0.5
CA A:TYR137 4.7 31.4 1.0
CB A:LEU114 4.8 29.5 1.0
CA A:TRP133 4.8 31.8 1.0
CB A:SER134 4.9 34.2 0.5
C A:SER134 5.0 32.1 1.0

Krypton binding site 5 out of 17 in 6eye

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Krypton binding site 5 out of 17 in the Crystal Structure of Murine Neuroglobin Under 150 Bar Krypton


Mono view


Stereo pair view

A full contact list of Krypton with other atoms in the Kr binding site number 5 of Crystal Structure of Murine Neuroglobin Under 150 Bar Krypton within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Kr206

b:32.5
occ:0.20
KR A:KR206 0.0 32.5 0.2
KR A:KR206 1.4 39.4 0.4
O A:GLY110 3.5 22.4 1.0
CB A:TYR137 3.5 28.8 1.0
CG A:LEU114 3.6 34.8 1.0
CD2 A:TYR137 3.6 31.0 1.0
CG A:TYR137 3.7 30.7 1.0
CD1 A:LEU114 3.7 36.5 1.0
C A:GLY110 3.8 20.6 1.0
CA A:SER134 3.8 31.3 0.5
CA A:GLY110 3.8 23.7 1.0
CA A:SER134 3.8 30.0 0.5
CD2 A:LEU114 3.9 32.6 1.0
OG A:SER134 4.1 29.7 0.5
OG A:SER134 4.2 38.3 0.5
O A:TRP133 4.3 31.1 1.0
O A:HOH351 4.3 53.4 1.0
N A:SER134 4.4 29.7 1.0
CB A:SER134 4.4 34.2 0.5
CB A:SER134 4.5 31.2 0.5
CE2 A:TYR137 4.5 32.3 1.0
C A:TRP133 4.6 29.1 1.0
O A:SER134 4.6 34.0 1.0
CD1 A:TYR137 4.7 32.4 1.0
C A:SER134 4.7 32.1 1.0
N A:GLU111 4.8 22.6 1.0
CB A:LEU114 4.9 29.5 1.0
CD2 A:LEU113 4.9 23.8 1.0

Krypton binding site 6 out of 17 in 6eye

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Krypton binding site 6 out of 17 in the Crystal Structure of Murine Neuroglobin Under 150 Bar Krypton


Mono view


Stereo pair view

A full contact list of Krypton with other atoms in the Kr binding site number 6 of Crystal Structure of Murine Neuroglobin Under 150 Bar Krypton within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Kr207

b:37.0
occ:0.26
CBC A:HEM202 3.1 37.6 1.0
CG1 A:VAL140 3.7 34.0 1.0
KR A:KR205 3.7 42.6 0.8
CG1 A:ILE72 3.8 31.1 1.0
KR A:KR204 3.9 37.8 1.0
CE1 A:TYR137 4.1 30.3 1.0
CD1 A:TYR137 4.2 32.4 1.0
CAC A:HEM202 4.4 31.2 1.0
CB A:VAL140 4.5 34.4 1.0
CG1 A:VAL71 4.5 33.4 1.0
CG2 A:VAL140 4.6 36.1 1.0
CE A:MET144 4.6 29.1 0.4
CD1 A:ILE72 4.7 31.3 1.0
CMC A:HEM202 4.7 39.2 1.0
CA A:ILE72 4.7 28.8 1.0
N A:ILE72 4.8 31.9 1.0
CB A:ILE72 4.9 28.3 1.0

Krypton binding site 7 out of 17 in 6eye

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Krypton binding site 7 out of 17 in the Crystal Structure of Murine Neuroglobin Under 150 Bar Krypton


Mono view


Stereo pair view

A full contact list of Krypton with other atoms in the Kr binding site number 7 of Crystal Structure of Murine Neuroglobin Under 150 Bar Krypton within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Kr208

b:31.0
occ:0.22
CZ A:PHE28 2.9 26.1 1.0
CE1 A:PHE28 3.5 31.5 1.0
CE2 A:PHE28 3.5 23.9 1.0
CMC A:HEM202 3.6 39.2 1.0
CHC A:HEM202 3.7 29.8 1.0
CG1 A:VAL109 3.7 26.5 1.0
CD2 A:LEU27 3.7 24.3 1.0
CG2 A:VAL109 4.0 26.1 1.0
C2C A:HEM202 4.0 34.6 1.0
C1C A:HEM202 4.1 28.0 1.0
CD2 A:LEU31 4.2 26.1 1.0
CAB A:HEM202 4.3 28.5 1.0
CB A:VAL109 4.4 25.2 1.0
CG2 A:VAL68 4.4 23.5 1.0
CG1 A:VAL68 4.4 28.1 1.0
C4B A:HEM202 4.5 28.7 1.0
CD1 A:PHE28 4.5 27.3 1.0
KR A:KR205 4.5 42.6 0.8
CD2 A:PHE28 4.5 23.6 1.0
C3B A:HEM202 4.8 29.6 1.0
CG A:PHE28 4.9 24.0 1.0

Krypton binding site 8 out of 17 in 6eye

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Krypton binding site 8 out of 17 in the Crystal Structure of Murine Neuroglobin Under 150 Bar Krypton


Mono view


Stereo pair view

A full contact list of Krypton with other atoms in the Kr binding site number 8 of Crystal Structure of Murine Neuroglobin Under 150 Bar Krypton within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Kr209

b:42.8
occ:0.30
KR A:KR209 0.0 42.8 0.3
KR A:KR209 2.1 34.8 0.2
N A:LEU92 3.5 45.8 1.0
CB A:SER91 3.5 50.3 1.0
C A:SER91 3.6 43.1 1.0
CA A:LEU92 3.7 35.1 1.0
CG A:LYS95 3.8 59.8 1.0
O A:SER91 3.9 47.8 1.0
CD A:LYS95 4.0 64.2 1.0
CD1 A:LEU92 4.2 35.1 1.0
CA A:SER91 4.2 41.9 1.0
CB A:LEU92 4.2 41.1 1.0
O A:TYR88 4.4 41.2 1.0
CE1 A:TYR88 4.5 42.5 1.0
O2D A:HEM202 4.6 47.7 1.0
CGD A:HEM202 4.6 43.8 1.0
OG A:SER91 4.6 64.8 1.0
CB A:LYS95 4.8 48.0 1.0
CD1 A:TYR88 4.9 42.6 1.0
CBD A:HEM202 4.9 36.3 1.0
C A:LEU92 4.9 41.4 1.0
CG A:LEU92 4.9 34.8 1.0
O1D A:HEM202 5.0 48.4 1.0

Krypton binding site 9 out of 17 in 6eye

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Krypton binding site 9 out of 17 in the Crystal Structure of Murine Neuroglobin Under 150 Bar Krypton


Mono view


Stereo pair view

A full contact list of Krypton with other atoms in the Kr binding site number 9 of Crystal Structure of Murine Neuroglobin Under 150 Bar Krypton within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Kr209

b:34.8
occ:0.21
KR A:KR209 0.0 34.8 0.2
KR A:KR209 2.1 42.8 0.3
CE1 A:TYR88 3.0 42.5 1.0
O A:HOH330 3.2 49.0 1.0
O2D A:HEM202 3.4 47.7 1.0
CZ A:TYR88 3.7 39.4 1.0
CD1 A:TYR88 3.8 42.6 1.0
OH A:TYR88 3.8 34.7 1.0
CGD A:HEM202 3.9 43.8 1.0
CD1 A:LEU92 4.1 35.1 1.0
CBD A:HEM202 4.3 36.3 1.0
O1D A:HEM202 4.7 48.4 1.0
CB A:LEU92 4.7 41.1 1.0
CA A:LEU92 4.8 35.1 1.0
CE2 A:TYR88 4.8 39.5 1.0
N A:LEU92 4.9 45.8 1.0
CG A:TYR88 4.9 37.6 1.0
O A:TYR88 4.9 41.2 1.0
CB A:SER91 5.0 50.3 1.0

Krypton binding site 10 out of 17 in 6eye

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Krypton binding site 10 out of 17 in the Crystal Structure of Murine Neuroglobin Under 150 Bar Krypton


Mono view


Stereo pair view

A full contact list of Krypton with other atoms in the Kr binding site number 10 of Crystal Structure of Murine Neuroglobin Under 150 Bar Krypton within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Kr210

b:33.2
occ:0.26
O A:HOH330 3.5 49.0 1.0
OH A:TYR88 3.6 34.7 1.0
KR A:KR211 3.7 36.7 0.2
CE1 A:TYR88 3.7 42.5 1.0
CZ A:TYR88 3.8 39.4 1.0
CD1 A:TYR88 4.6 42.6 1.0
CE2 A:TYR88 4.7 39.5 1.0

Reference:

N.Colloc'h, P.Carpentier, L.C.Montemiglio, B.Vallone, T.Prange. Mapping Hydrophobic Tunnels and Cavities in Neuroglobin with Noble Gas Under Pressure. Biophys. J. V. 113 2199 2017.
ISSN: ESSN 1542-0086
PubMed: 29108649
DOI: 10.1016/J.BPJ.2017.10.014
Page generated: Mon Dec 14 02:54:49 2020

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