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Zinc in PDB 2g87: Crystallographic Model of Bathorhodopsin

Protein crystallography data

The structure of Crystallographic Model of Bathorhodopsin, PDB code: 2g87 was solved by H.Nakamichi, T.Okada, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.60
Space group P 41
Cell size a, b, c (Å), α, β, γ (°) 96.490, 96.490, 150.400, 90.00, 90.00, 90.00
R / Rfree (%) 17.8 / 18.1

Other elements in 2g87:

The structure of Crystallographic Model of Bathorhodopsin also contains other interesting chemical elements:

Mercury (Hg) 6 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystallographic Model of Bathorhodopsin (pdb code 2g87). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 7 binding sites of Zinc where determined in the Crystallographic Model of Bathorhodopsin, PDB code: 2g87:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7;

Zinc binding site 1 out of 7 in 2g87

Go back to Zinc Binding Sites List in 2g87
Zinc binding site 1 out of 7 in the Crystallographic Model of Bathorhodopsin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystallographic Model of Bathorhodopsin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn957

b:42.0
occ:0.66
NE2 A:GLN279 1.8 53.3 1.0
OE2 A:GLU201 2.1 52.8 1.0
OE1 A:GLU201 2.3 52.9 1.0
CD A:GLU201 2.5 52.5 1.0
CD A:GLN279 2.7 54.4 1.0
OE1 A:GLN279 2.9 56.0 1.0
CG A:GLU201 4.0 52.5 1.0
CG A:GLN279 4.1 53.2 1.0
O A:PHE276 4.2 49.5 1.0
CE1 A:PHE276 4.3 43.2 1.0
CG A:PRO194 4.5 57.7 1.0
CZ A:PHE276 4.5 41.7 1.0
O A:HOH2057 4.7 78.3 1.0
CD1 A:PHE276 4.8 44.9 1.0
CB A:PRO194 4.9 57.3 1.0
CB A:GLU201 5.0 53.1 1.0

Zinc binding site 2 out of 7 in 2g87

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Zinc binding site 2 out of 7 in the Crystallographic Model of Bathorhodopsin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystallographic Model of Bathorhodopsin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn959

b:73.6
occ:0.85
NZ A:LYS311 1.9 65.9 1.0
CE1 B:HIS100 2.6 57.7 1.0
N A:ASP330 2.6 0.0 1.0
NE2 B:HIS100 3.0 58.0 1.0
CE A:LYS311 3.3 66.1 1.0
CA A:GLY329 3.3 0.4 1.0
C A:GLY329 3.3 0.9 1.0
CB A:ASP330 3.4 0.5 1.0
OD2 A:ASP330 3.5 0.9 1.0
CG A:ASP330 3.5 0.9 1.0
CA A:ASP330 3.5 0.3 1.0
ND1 B:HIS100 3.8 56.9 1.0
N A:ASP331 4.1 0.8 1.0
OD1 A:ASP330 4.2 0.9 1.0
CD A:LYS311 4.2 65.6 1.0
C A:ASP330 4.3 0.2 1.0
O A:ASP331 4.3 0.2 1.0
CD2 B:HIS100 4.3 56.5 1.0
CE1 B:TYR96 4.4 60.5 1.0
O A:GLY329 4.4 0.2 1.0
OH B:TYR96 4.5 62.0 1.0
NH2 A:ARG314 4.5 51.5 1.0
ND2 A:ASN315 4.6 61.9 1.0
CG A:LYS311 4.7 63.3 1.0
CG B:HIS100 4.7 55.6 1.0
N A:GLY329 4.8 0.1 1.0
CZ B:TYR96 4.8 61.5 1.0
NE A:ARG314 4.8 50.6 1.0

Zinc binding site 3 out of 7 in 2g87

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Zinc binding site 3 out of 7 in the Crystallographic Model of Bathorhodopsin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystallographic Model of Bathorhodopsin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn962

b:63.5
occ:0.62
ND1 A:HIS211 2.3 55.1 1.0
O A:MET163 2.6 58.1 1.0
NE1 A:TRP126 2.6 55.6 1.0
OE1 A:GLU122 3.0 52.0 1.0
CE1 A:HIS211 3.0 56.1 1.0
CG A:HIS211 3.0 54.6 1.0
CB A:CYS167 3.2 57.2 1.0
C A:MET163 3.3 57.5 1.0
CD1 A:TRP126 3.4 55.5 1.0
CD A:GLU122 3.5 51.3 1.0
CB A:HIS211 3.6 54.2 1.0
CA A:ALA164 3.6 56.5 1.0
CG A:GLU122 3.7 50.1 1.0
CE2 A:TRP126 3.7 55.7 1.0
N A:ALA164 3.7 56.9 1.0
NE2 A:HIS211 3.8 56.4 1.0
CD2 A:HIS211 3.8 55.6 1.0
CB A:GLU122 3.9 49.2 1.0
SG A:CYS167 4.2 64.3 1.0
CZ2 A:TRP126 4.2 55.8 1.0
O A:ALA164 4.3 56.7 1.0
N A:CYS167 4.3 55.4 1.0
C A:ALA164 4.3 56.5 1.0
CA A:CYS167 4.3 55.5 1.0
CA A:MET163 4.4 57.5 1.0
OE2 A:GLU122 4.4 50.9 1.0
CB A:MET163 4.4 58.0 1.0
CA A:HIS211 4.6 54.6 1.0
CG A:TRP126 4.7 54.3 1.0
CB A:ALA164 4.7 56.6 1.0
CD2 A:TRP126 4.8 55.3 1.0
O A:GLU122 4.9 49.6 1.0
CA A:GLU122 4.9 49.5 1.0

Zinc binding site 4 out of 7 in 2g87

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Zinc binding site 4 out of 7 in the Crystallographic Model of Bathorhodopsin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystallographic Model of Bathorhodopsin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2011

b:50.9
occ:0.68
NE2 A:HIS195 2.3 55.0 1.0
OE1 A:GLU197 2.4 74.2 1.0
CD A:GLU197 3.2 71.5 1.0
CD2 A:HIS195 3.2 54.4 1.0
CE1 A:HIS195 3.3 55.3 1.0
OE2 A:GLU197 3.5 73.2 1.0
O A:PRO7 4.0 49.3 1.0
O A:HOH2062 4.3 47.3 1.0
ND1 A:HIS195 4.4 55.5 1.0
CG A:HIS195 4.4 54.6 1.0
CG A:GLU197 4.4 67.1 1.0
CB A:GLU197 4.5 60.9 1.0
NH1 A:ARG177 4.6 50.0 1.0
C A:PRO7 4.9 49.4 1.0

Zinc binding site 5 out of 7 in 2g87

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Zinc binding site 5 out of 7 in the Crystallographic Model of Bathorhodopsin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystallographic Model of Bathorhodopsin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn956

b:56.2
occ:0.68
NE2 B:HIS195 2.0 60.1 1.0
OE1 B:GLU197 2.5 78.8 1.0
CE1 B:HIS195 3.0 60.5 1.0
CD B:GLU197 3.0 77.2 1.0
OE2 B:GLU197 3.0 78.8 1.0
CD2 B:HIS195 3.1 61.1 1.0
O B:PRO7 3.8 56.0 1.0
ND1 B:HIS195 4.1 61.1 1.0
CG B:HIS195 4.2 60.4 1.0
CG B:GLU197 4.3 73.0 1.0
NH1 B:ARG177 4.4 49.1 1.0
CB B:GLU197 4.5 67.8 1.0
CB B:PRO7 4.7 54.4 1.0
C B:PRO7 4.7 55.2 1.0
CA B:PRO7 4.7 54.3 1.0

Zinc binding site 6 out of 7 in 2g87

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Zinc binding site 6 out of 7 in the Crystallographic Model of Bathorhodopsin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystallographic Model of Bathorhodopsin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn958

b:36.6
occ:0.51
NE2 B:GLN279 1.8 53.0 1.0
OE2 B:GLU201 2.2 58.6 1.0
OE1 B:GLU201 2.4 57.4 1.0
CD B:GLU201 2.6 58.5 1.0
CD B:GLN279 2.9 53.0 1.0
OE1 B:GLN279 3.4 54.1 1.0
O B:PHE276 3.8 54.5 1.0
CG B:GLN279 4.0 52.6 1.0
CG B:GLU201 4.1 59.2 1.0
CE1 B:PHE276 4.4 48.5 1.0
CZ B:PHE276 4.5 47.6 1.0
CD1 B:PHE276 4.8 50.0 1.0
CG B:PRO194 4.9 59.4 1.0
CE2 B:PHE276 5.0 48.3 1.0
C B:PHE276 5.0 52.7 1.0

Zinc binding site 7 out of 7 in 2g87

Go back to Zinc Binding Sites List in 2g87
Zinc binding site 7 out of 7 in the Crystallographic Model of Bathorhodopsin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystallographic Model of Bathorhodopsin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn963

b:72.5
occ:0.68
ND1 B:HIS211 2.3 68.5 1.0
NE1 B:TRP126 2.5 68.8 1.0
CE1 B:HIS211 2.7 69.0 1.0
O B:MET163 2.8 64.4 1.0
OE1 B:GLU122 2.8 63.4 1.0
C B:MET163 3.1 64.9 1.0
CG B:HIS211 3.1 67.6 1.0
CD1 B:TRP126 3.3 68.8 1.0
N B:ALA164 3.4 64.6 1.0
CD B:GLU122 3.5 61.7 1.0
CA B:ALA164 3.5 63.9 1.0
NE2 B:HIS211 3.5 69.0 1.0
CE2 B:TRP126 3.5 69.2 1.0
CG B:GLU122 3.6 59.9 1.0
CB B:CYS167 3.7 64.5 1.0
CD2 B:HIS211 3.8 69.1 1.0
CB B:GLU122 3.8 58.0 1.0
CB B:HIS211 3.8 64.9 1.0
CB B:MET163 3.9 66.2 1.0
CA B:MET163 4.0 65.1 1.0
CZ2 B:TRP126 4.1 70.1 1.0
C B:ALA164 4.2 63.9 1.0
O B:ALA164 4.2 64.5 1.0
N B:CYS167 4.4 64.0 1.0
CG B:TRP126 4.5 68.0 1.0
OE2 B:GLU122 4.5 61.4 1.0
CD2 B:TRP126 4.6 69.0 1.0
CA B:CYS167 4.7 63.3 1.0
SG B:CYS167 4.7 72.7 1.0
CB B:ALA164 4.8 63.8 1.0
CA B:HIS211 4.8 62.8 1.0
CA B:GLU122 4.9 58.0 1.0

Reference:

H.Nakamichi, T.Okada. Crystallographic Analysis of Primary Visual Photochemistry Angew.Chem.Int.Ed.Engl. V. 45 4270 2006.
ISSN: ISSN 1433-7851
PubMed: 16586416
DOI: 10.1002/ANIE.200600595
Page generated: Wed Dec 16 03:28:59 2020

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