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Calcium in PDB 1gu6: Structure of the Periplasmic Cytochrome C Nitrite Reductase From Escherichia Coli

Protein crystallography data

The structure of Structure of the Periplasmic Cytochrome C Nitrite Reductase From Escherichia Coli, PDB code: 1gu6 was solved by V.A.Bamford, H.C.Angove, H.E.Seward, A.J.Thomson, J.A.Cole, J.N.Butt, A.M.Hemmings, D.J.Richardson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20 / 2.5
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 81.472, 90.837, 293.874, 90.00, 90.00, 90.00
R / Rfree (%) 20.3 / 24.3

Other elements in 1gu6:

The structure of Structure of the Periplasmic Cytochrome C Nitrite Reductase From Escherichia Coli also contains other interesting chemical elements:

Iron (Fe) 20 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Structure of the Periplasmic Cytochrome C Nitrite Reductase From Escherichia Coli (pdb code 1gu6). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Structure of the Periplasmic Cytochrome C Nitrite Reductase From Escherichia Coli, PDB code: 1gu6:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 1gu6

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Calcium binding site 1 out of 8 in the Structure of the Periplasmic Cytochrome C Nitrite Reductase From Escherichia Coli


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of the Periplasmic Cytochrome C Nitrite Reductase From Escherichia Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1479

b:30.3
occ:1.00
 O A:HOH2081 2.2 33.9 1.0
OE1 A:GLN263 2.2 31.7 1.0
O A:LYS261 2.4 23.1 1.0
O A:TYR216 2.4 33.3 1.0
OE2 A:GLU215 2.5 27.6 1.0
OE1 A:GLU215 2.6 27.0 1.0
CD A:GLU215 2.9 27.6 1.0
CD A:GLN263 3.4 29.8 1.0
C A:LYS261 3.6 24.2 1.0
C A:TYR216 3.6 30.8 1.0
NE2 A:GLN263 3.9 34.2 1.0
OH A:TYR242 4.0 27.6 1.0
N A:TYR216 4.1 27.7 1.0
CA A:ALA262 4.3 25.9 1.0
N A:GLN263 4.3 26.4 1.0
CG A:GLU215 4.4 26.3 1.0
N A:ALA262 4.4 25.7 1.0
C A:ALA262 4.4 27.8 1.0
OD2 A:ASP249 4.5 31.5 1.0
CA A:TYR216 4.5 28.6 1.0
N A:TYR217 4.5 31.8 1.0
OD1 A:ASP249 4.5 29.5 1.0
CA A:TYR217 4.6 31.6 1.0
CA A:LYS261 4.6 27.0 1.0
CG A:GLN263 4.6 29.5 1.0
CB A:TYR217 4.6 33.4 1.0
CB A:LYS261 4.7 27.9 1.0
CB A:GLN263 4.7 28.2 1.0
CG A:ASP249 4.8 28.8 1.0
N A:LYS261 4.8 28.9 1.0
CZ A:TYR242 4.9 28.2 1.0
CZ3 A:TRP379 4.9 24.3 1.0

Calcium binding site 2 out of 8 in 1gu6

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Calcium binding site 2 out of 8 in the Structure of the Periplasmic Cytochrome C Nitrite Reductase From Escherichia Coli


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of the Periplasmic Cytochrome C Nitrite Reductase From Escherichia Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1480

b:51.4
occ:1.00
 O1A A:HEC1485 2.3 46.0 1.0
O1A A:HEC1484 2.4 32.2 1.0
O A:PRO91 2.6 29.0 1.0
O A:HOH2160 2.7 36.8 1.0
CGA A:HEC1485 3.3 42.8 1.0
CGA A:HEC1484 3.6 33.5 1.0
O2A A:HEC1485 3.6 44.2 1.0
C A:PRO91 3.7 30.1 1.0
O A:HOH2161 3.9 31.3 1.0
O2A A:HEC1484 4.1 34.1 1.0
CA A:ARG92 4.5 30.6 1.0
CBA A:HEC1485 4.6 38.7 1.0
N A:ARG92 4.6 30.5 1.0
CA A:PRO91 4.6 31.0 1.0
CB A:PRO91 4.6 29.9 1.0
O A:HOH2098 4.6 31.1 1.0
CBA A:HEC1484 4.7 28.9 1.0
N A:PRO91 4.7 30.8 1.0
CD A:PRO91 4.7 28.8 1.0
O A:HOH2013 4.7 52.6 1.0
CAA A:HEC1484 4.8 26.8 1.0

Calcium binding site 3 out of 8 in 1gu6

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Calcium binding site 3 out of 8 in the Structure of the Periplasmic Cytochrome C Nitrite Reductase From Escherichia Coli


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of the Periplasmic Cytochrome C Nitrite Reductase From Escherichia Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca1479

b:34.0
occ:1.00
 OE1 C:GLN263 2.3 31.8 1.0
O C:LYS261 2.4 31.4 1.0
O C:TYR216 2.4 35.0 1.0
O C:HOH2060 2.4 26.7 1.0
OE2 C:GLU215 2.5 33.0 1.0
OE1 C:GLU215 2.7 30.4 1.0
CD C:GLU215 2.9 32.4 1.0
CD C:GLN263 3.4 30.2 1.0
C C:LYS261 3.6 29.9 1.0
C C:TYR216 3.6 34.0 1.0
NE2 C:GLN263 3.9 34.0 1.0
OH C:TYR242 4.0 31.0 1.0
N C:TYR216 4.2 32.0 1.0
CA C:ALA262 4.3 28.3 1.0
OD2 C:ASP249 4.3 33.6 1.0
N C:GLN263 4.4 27.7 1.0
N C:ALA262 4.4 29.6 1.0
C C:ALA262 4.4 29.6 1.0
OD1 C:ASP249 4.4 33.8 1.0
CG C:GLU215 4.4 29.0 1.0
N C:TYR217 4.5 34.0 1.0
CA C:TYR217 4.6 34.5 1.0
CA C:TYR216 4.6 32.1 1.0
CA C:LYS261 4.6 29.6 1.0
CB C:TYR217 4.6 34.6 1.0
CG C:GLN263 4.6 26.8 1.0
CB C:LYS261 4.7 29.3 1.0
CG C:ASP249 4.7 33.4 1.0
CB C:GLN263 4.7 23.8 1.0
N C:LYS261 4.8 31.1 1.0
CZ3 C:TRP379 4.9 26.3 1.0
CZ C:TYR242 4.9 32.4 1.0
O C:ALA262 5.0 32.8 1.0

Calcium binding site 4 out of 8 in 1gu6

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Calcium binding site 4 out of 8 in the Structure of the Periplasmic Cytochrome C Nitrite Reductase From Escherichia Coli


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structure of the Periplasmic Cytochrome C Nitrite Reductase From Escherichia Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca1480

b:54.1
occ:1.00
 O1A C:HEC1485 2.4 44.8 1.0
O1A C:HEC1484 2.5 32.2 1.0
O C:PRO91 2.6 34.9 1.0
O C:HOH2120 2.7 32.4 1.0
CGA C:HEC1485 3.4 41.1 1.0
O2A C:HEC1485 3.7 43.5 1.0
CGA C:HEC1484 3.7 33.5 1.0
C C:PRO91 3.7 34.4 1.0
O2A C:HEC1484 4.2 32.9 1.0
CA C:ARG92 4.5 32.7 1.0
CA C:PRO91 4.6 33.7 1.0
N C:ARG92 4.6 34.6 1.0
CB C:PRO91 4.6 32.5 1.0
N C:PRO91 4.6 34.3 1.0
CD C:PRO91 4.6 33.8 1.0
CBA C:HEC1485 4.6 38.0 1.0
CBA C:HEC1484 4.8 30.0 1.0
CAA C:HEC1484 4.9 27.5 1.0
CB C:LYS90 5.0 34.3 1.0

Calcium binding site 5 out of 8 in 1gu6

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Calcium binding site 5 out of 8 in the Structure of the Periplasmic Cytochrome C Nitrite Reductase From Escherichia Coli


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Structure of the Periplasmic Cytochrome C Nitrite Reductase From Escherichia Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca1479

b:26.8
occ:1.00
 O E:HOH2109 2.1 27.2 1.0
OE1 E:GLN263 2.3 31.4 1.0
O E:LYS261 2.3 26.0 1.0
O E:TYR216 2.4 24.0 1.0
OE2 E:GLU215 2.5 25.8 1.0
OE1 E:GLU215 2.7 25.5 1.0
O E:HOH2111 2.7 32.1 1.0
CD E:GLU215 2.9 23.9 1.0
CD E:GLN263 3.4 30.6 1.0
C E:LYS261 3.5 25.4 1.0
C E:TYR216 3.6 26.1 1.0
OH E:TYR242 4.0 26.8 1.0
NE2 E:GLN263 4.0 31.1 1.0
N E:TYR216 4.1 24.5 1.0
CA E:ALA262 4.3 24.4 1.0
OD2 E:ASP249 4.3 29.0 1.0
N E:ALA262 4.3 23.0 1.0
N E:GLN263 4.4 22.4 1.0
CG E:GLU215 4.4 22.4 1.0
C E:ALA262 4.4 23.7 1.0
OD1 E:ASP249 4.5 29.0 1.0
N E:TYR217 4.5 27.1 1.0
CA E:TYR216 4.5 25.1 1.0
CA E:LYS261 4.5 24.0 1.0
CA E:TYR217 4.6 28.0 1.0
CB E:TYR217 4.6 28.3 1.0
CB E:LYS261 4.7 24.1 1.0
CG E:GLN263 4.7 27.4 1.0
CG E:ASP249 4.8 30.8 1.0
N E:LYS261 4.8 25.9 1.0
CB E:GLN263 4.8 23.2 1.0
CZ E:TYR242 4.9 29.2 1.0
CZ3 E:TRP379 4.9 23.3 1.0

Calcium binding site 6 out of 8 in 1gu6

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Calcium binding site 6 out of 8 in the Structure of the Periplasmic Cytochrome C Nitrite Reductase From Escherichia Coli


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Structure of the Periplasmic Cytochrome C Nitrite Reductase From Escherichia Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca1480

b:48.5
occ:1.00
 O1A E:HEC1484 2.4 29.1 1.0
O1A E:HEC1485 2.4 41.1 1.0
O E:PRO91 2.6 30.5 1.0
O E:HOH2186 2.7 22.8 1.0
CGA E:HEC1485 3.5 35.6 1.0
CGA E:HEC1484 3.6 31.3 1.0
C E:PRO91 3.7 29.3 1.0
O2A E:HEC1485 3.8 35.9 1.0
O2A E:HEC1484 4.1 31.6 1.0
O E:HOH2017 4.3 28.2 1.0
CA E:ARG92 4.4 27.2 1.0
O E:HOH2131 4.5 36.3 1.0
N E:ARG92 4.5 27.9 1.0
CA E:PRO91 4.6 28.9 1.0
CB E:PRO91 4.6 28.9 1.0
CBA E:HEC1485 4.7 34.1 1.0
N E:PRO91 4.7 29.1 1.0
CBA E:HEC1484 4.7 26.0 1.0
CD E:PRO91 4.8 30.0 1.0
CAA E:HEC1484 4.9 25.8 1.0

Calcium binding site 7 out of 8 in 1gu6

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Calcium binding site 7 out of 8 in the Structure of the Periplasmic Cytochrome C Nitrite Reductase From Escherichia Coli


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Structure of the Periplasmic Cytochrome C Nitrite Reductase From Escherichia Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Ca1479

b:26.5
occ:1.00
 OE1 G:GLN263 2.2 27.5 1.0
O G:LYS261 2.3 23.9 1.0
O G:HOH2112 2.4 33.5 1.0
O G:TYR216 2.5 25.7 1.0
O G:HOH2110 2.6 33.9 1.0
OE2 G:GLU215 2.6 27.9 1.0
OE1 G:GLU215 2.6 26.6 1.0
CD G:GLU215 2.9 26.0 1.0
CD G:GLN263 3.4 29.5 1.0
C G:LYS261 3.5 25.8 1.0
C G:TYR216 3.7 25.4 1.0
NE2 G:GLN263 3.9 32.1 1.0
OH G:TYR242 4.0 27.7 1.0
N G:TYR216 4.2 25.3 1.0
CA G:ALA262 4.2 26.4 1.0
N G:ALA262 4.3 26.6 1.0
OD2 G:ASP249 4.3 34.2 1.0
N G:GLN263 4.4 23.2 1.0
C G:ALA262 4.4 25.5 1.0
CG G:GLU215 4.4 23.7 1.0
CA G:LYS261 4.5 25.9 1.0
OD1 G:ASP249 4.5 26.8 1.0
N G:TYR217 4.5 26.9 1.0
CA G:TYR216 4.6 25.7 1.0
CA G:TYR217 4.6 29.5 1.0
CB G:LYS261 4.6 23.5 1.0
CB G:TYR217 4.6 31.3 1.0
CG G:GLN263 4.6 28.6 1.0
N G:LYS261 4.7 26.2 1.0
CG G:ASP249 4.8 31.3 1.0
CB G:GLN263 4.8 25.6 1.0
CZ3 G:TRP379 4.9 25.4 1.0
CZ G:TYR242 4.9 30.7 1.0

Calcium binding site 8 out of 8 in 1gu6

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Calcium binding site 8 out of 8 in the Structure of the Periplasmic Cytochrome C Nitrite Reductase From Escherichia Coli


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Structure of the Periplasmic Cytochrome C Nitrite Reductase From Escherichia Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Ca1480

b:47.1
occ:1.00
 O1A G:HEC1484 2.4 28.6 1.0
O1A G:HEC1485 2.4 43.6 1.0
O G:PRO91 2.5 31.2 1.0
O G:HOH2198 2.7 35.2 1.0
CGA G:HEC1485 3.4 37.4 1.0
C G:PRO91 3.6 29.5 1.0
CGA G:HEC1484 3.6 29.7 1.0
O2A G:HEC1485 3.6 37.5 1.0
O2A G:HEC1484 4.1 29.2 1.0
CA G:ARG92 4.3 26.8 1.0
O G:HOH2201 4.3 41.5 1.0
N G:ARG92 4.4 28.7 1.0
CA G:PRO91 4.5 29.8 1.0
CB G:PRO91 4.5 30.2 1.0
N G:PRO91 4.6 30.3 1.0
O G:HOH2016 4.6 32.7 1.0
CD G:PRO91 4.6 29.0 1.0
CBA G:HEC1485 4.6 36.0 1.0
CBA G:HEC1484 4.7 25.7 1.0
O G:HOH2199 4.8 28.4 1.0
CAA G:HEC1484 4.8 25.1 1.0
C G:LYS90 5.0 30.8 1.0
CB G:LYS90 5.0 32.0 1.0
CG G:PRO91 5.0 28.5 1.0

Reference:

V.A.Bamford, H.C.Angove, H.E.Seward, A.J.Thomson, J.A.Cole, J.N.Butt, A.M.Hemmings, D.J.Richardson. Structure and Spectroscopy of the Periplasmic Cytochrome C Nitrite Reductase From Escherichia Coli Biochemistry V. 41 2921 2002.
ISSN: ISSN 0006-2960
PubMed: 11863430
DOI: 10.1021/BI015765D
Page generated: Thu Jul 11 08:50:51 2024

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