Calcium in PDB 6qyc: Crystal Structure of Mtrc From Shewanella Baltica OS185
Protein crystallography data
The structure of Crystal Structure of Mtrc From Shewanella Baltica OS185, PDB code: 6qyc
was solved by
T.A.Clarke,
M.J.Edwards,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
87.20 /
2.29
|
Space group
|
P 21 21 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
90.520,
291.500,
87.200,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
18.3 /
22.8
|
Other elements in 6qyc:
The structure of Crystal Structure of Mtrc From Shewanella Baltica OS185 also contains other interesting chemical elements:
Calcium Binding Sites:
The binding sites of Calcium atom in the Crystal Structure of Mtrc From Shewanella Baltica OS185
(pdb code 6qyc). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the
Crystal Structure of Mtrc From Shewanella Baltica OS185, PDB code: 6qyc:
Jump to Calcium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Calcium binding site 1 out
of 8 in 6qyc
Go back to
Calcium Binding Sites List in 6qyc
Calcium binding site 1 out
of 8 in the Crystal Structure of Mtrc From Shewanella Baltica OS185
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 1 of Crystal Structure of Mtrc From Shewanella Baltica OS185 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca811
b:47.3
occ:1.00
|
N
|
A:GLY542
|
3.0
|
48.3
|
1.0
|
O
|
A:HOH957
|
3.1
|
46.0
|
1.0
|
N
|
A:GLY546
|
3.2
|
40.5
|
1.0
|
N
|
A:THR538
|
3.3
|
44.7
|
1.0
|
N
|
A:ASN544
|
3.3
|
39.3
|
1.0
|
CA
|
A:GLY542
|
3.4
|
38.4
|
1.0
|
N
|
A:LYS545
|
3.5
|
39.2
|
1.0
|
C
|
A:GLY542
|
3.6
|
43.6
|
1.0
|
CA
|
A:GLY537
|
3.6
|
38.8
|
1.0
|
CA
|
A:GLY546
|
3.7
|
39.1
|
1.0
|
C
|
A:ASN544
|
3.7
|
39.9
|
1.0
|
OG1
|
A:THR538
|
3.7
|
44.6
|
1.0
|
CA
|
A:ASN544
|
3.8
|
41.9
|
1.0
|
N
|
A:ALA543
|
3.8
|
40.4
|
1.0
|
CB
|
A:ASN544
|
3.8
|
38.0
|
1.0
|
N
|
A:SER541
|
3.9
|
45.1
|
1.0
|
C
|
A:GLY537
|
4.0
|
45.3
|
1.0
|
O
|
A:GLY542
|
4.1
|
42.0
|
1.0
|
C
|
A:LYS545
|
4.2
|
44.2
|
1.0
|
C
|
A:SER541
|
4.2
|
50.6
|
1.0
|
C
|
A:ALA540
|
4.2
|
46.8
|
1.0
|
CA
|
A:LYS545
|
4.3
|
48.3
|
1.0
|
CA
|
A:THR538
|
4.3
|
45.6
|
1.0
|
O
|
A:ASN544
|
4.4
|
45.2
|
1.0
|
CB
|
A:ALA540
|
4.4
|
38.8
|
1.0
|
N
|
A:ALA540
|
4.4
|
44.7
|
1.0
|
C
|
A:ALA543
|
4.4
|
43.2
|
1.0
|
C
|
A:THR538
|
4.5
|
46.4
|
1.0
|
CA
|
A:SER541
|
4.5
|
44.0
|
1.0
|
CA
|
A:ALA540
|
4.5
|
42.9
|
1.0
|
O
|
A:THR538
|
4.6
|
43.0
|
1.0
|
CB
|
A:THR538
|
4.6
|
45.5
|
1.0
|
O
|
A:ALA540
|
4.7
|
51.8
|
1.0
|
CA
|
A:ALA543
|
4.7
|
42.6
|
1.0
|
CG
|
A:ASN544
|
4.8
|
44.6
|
1.0
|
ND2
|
A:ASN544
|
4.9
|
41.3
|
1.0
|
N
|
A:GLY537
|
4.9
|
42.7
|
1.0
|
O
|
A:HOH973
|
4.9
|
41.7
|
1.0
|
|
Calcium binding site 2 out
of 8 in 6qyc
Go back to
Calcium Binding Sites List in 6qyc
Calcium binding site 2 out
of 8 in the Crystal Structure of Mtrc From Shewanella Baltica OS185
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 2 of Crystal Structure of Mtrc From Shewanella Baltica OS185 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca812
b:77.1
occ:1.00
|
O
|
A:GLN511
|
2.5
|
51.9
|
1.0
|
O
|
A:HOH984
|
2.5
|
53.4
|
1.0
|
O
|
A:HOH1163
|
2.6
|
44.6
|
1.0
|
OE1
|
A:GLU464
|
2.7
|
49.2
|
1.0
|
O
|
A:HOH1174
|
2.7
|
55.0
|
1.0
|
O
|
A:HOH962
|
2.8
|
47.4
|
1.0
|
OE2
|
A:GLU464
|
3.4
|
50.4
|
1.0
|
CD
|
A:GLU464
|
3.4
|
52.4
|
1.0
|
O
|
A:LEU465
|
3.6
|
52.2
|
1.0
|
O
|
A:HOH1193
|
3.7
|
57.0
|
1.0
|
C
|
A:GLN511
|
3.7
|
47.7
|
1.0
|
OE1
|
A:GLN333
|
4.4
|
64.4
|
1.0
|
CA
|
A:VAL512
|
4.5
|
46.5
|
1.0
|
N
|
A:VAL512
|
4.6
|
43.2
|
1.0
|
CG
|
A:GLN511
|
4.6
|
47.2
|
1.0
|
N
|
A:LEU465
|
4.6
|
43.7
|
1.0
|
CA
|
A:GLN511
|
4.7
|
42.6
|
1.0
|
C
|
A:LEU465
|
4.7
|
46.2
|
1.0
|
CG
|
A:GLU464
|
4.9
|
48.2
|
1.0
|
O
|
A:MET332
|
4.9
|
50.4
|
1.0
|
C
|
A:VAL512
|
5.0
|
42.0
|
1.0
|
|
Calcium binding site 3 out
of 8 in 6qyc
Go back to
Calcium Binding Sites List in 6qyc
Calcium binding site 3 out
of 8 in the Crystal Structure of Mtrc From Shewanella Baltica OS185
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 3 of Crystal Structure of Mtrc From Shewanella Baltica OS185 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca811
b:45.7
occ:1.00
|
N
|
B:GLY542
|
3.0
|
44.5
|
1.0
|
O
|
B:HOH905
|
3.2
|
45.5
|
1.0
|
N
|
B:THR538
|
3.3
|
44.9
|
1.0
|
N
|
B:ASN544
|
3.3
|
40.0
|
1.0
|
N
|
B:GLY546
|
3.3
|
42.2
|
1.0
|
CA
|
B:GLY542
|
3.4
|
43.8
|
1.0
|
C
|
B:GLY542
|
3.5
|
47.9
|
1.0
|
N
|
B:LYS545
|
3.6
|
37.5
|
1.0
|
CA
|
B:GLY537
|
3.7
|
43.4
|
1.0
|
OG1
|
B:THR538
|
3.7
|
45.5
|
1.0
|
N
|
B:ALA543
|
3.7
|
46.9
|
1.0
|
CB
|
B:ASN544
|
3.8
|
39.2
|
1.0
|
CA
|
B:ASN544
|
3.8
|
41.0
|
1.0
|
C
|
B:ASN544
|
3.8
|
41.4
|
1.0
|
CA
|
B:GLY546
|
3.8
|
43.6
|
1.0
|
N
|
B:SER541
|
3.8
|
42.3
|
1.0
|
C
|
B:GLY537
|
4.0
|
48.2
|
1.0
|
CB
|
B:ALA540
|
4.0
|
48.2
|
1.0
|
C
|
B:ALA540
|
4.1
|
48.8
|
1.0
|
O
|
B:GLY542
|
4.1
|
45.1
|
1.0
|
C
|
B:SER541
|
4.1
|
48.7
|
1.0
|
N
|
B:ALA540
|
4.3
|
47.2
|
1.0
|
CA
|
B:THR538
|
4.3
|
47.3
|
1.0
|
C
|
B:LYS545
|
4.3
|
37.6
|
1.0
|
CA
|
B:ALA540
|
4.3
|
45.9
|
1.0
|
CA
|
B:LYS545
|
4.4
|
39.6
|
1.0
|
C
|
B:ALA543
|
4.4
|
45.9
|
1.0
|
C
|
B:THR538
|
4.4
|
46.5
|
1.0
|
CA
|
B:SER541
|
4.4
|
48.3
|
1.0
|
O
|
B:ASN544
|
4.5
|
41.0
|
1.0
|
O
|
B:THR538
|
4.5
|
46.4
|
1.0
|
CB
|
B:THR538
|
4.6
|
47.1
|
1.0
|
O
|
B:ALA540
|
4.6
|
49.5
|
1.0
|
CA
|
B:ALA543
|
4.6
|
47.5
|
1.0
|
CG
|
B:ASN544
|
4.7
|
43.0
|
1.0
|
ND2
|
B:ASN544
|
4.8
|
43.8
|
1.0
|
O2D
|
B:HEC807
|
5.0
|
45.4
|
1.0
|
N
|
B:GLY537
|
5.0
|
39.3
|
1.0
|
O
|
B:HOH991
|
5.0
|
41.5
|
1.0
|
|
Calcium binding site 4 out
of 8 in 6qyc
Go back to
Calcium Binding Sites List in 6qyc
Calcium binding site 4 out
of 8 in the Crystal Structure of Mtrc From Shewanella Baltica OS185
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 4 of Crystal Structure of Mtrc From Shewanella Baltica OS185 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca812
b:77.3
occ:1.00
|
O
|
B:HOH996
|
2.6
|
50.7
|
1.0
|
OG
|
B:SER197
|
2.8
|
50.2
|
1.0
|
N
|
B:ALA194
|
2.8
|
49.1
|
1.0
|
O
|
B:CYS257
|
2.9
|
47.9
|
1.0
|
CB
|
B:SER197
|
3.4
|
43.6
|
1.0
|
CA
|
B:VAL193
|
3.5
|
44.4
|
1.0
|
O
|
B:ALA194
|
3.6
|
40.2
|
1.0
|
C
|
B:VAL193
|
3.6
|
44.3
|
1.0
|
CA
|
B:ALA194
|
3.7
|
44.9
|
1.0
|
C
|
B:CYS257
|
3.8
|
44.4
|
1.0
|
CB
|
B:ALA194
|
3.9
|
42.1
|
1.0
|
CB
|
B:VAL193
|
3.9
|
47.1
|
1.0
|
C
|
B:ALA194
|
4.1
|
44.8
|
1.0
|
CG1
|
B:VAL193
|
4.3
|
43.4
|
1.0
|
CA
|
B:CYS257
|
4.5
|
45.1
|
1.0
|
O
|
B:ILE192
|
4.5
|
37.2
|
1.0
|
N
|
B:ALA259
|
4.6
|
48.6
|
1.0
|
O
|
B:ALA259
|
4.6
|
52.2
|
1.0
|
CA
|
B:SER197
|
4.7
|
44.5
|
1.0
|
N
|
B:HIS258
|
4.7
|
43.6
|
1.0
|
N
|
B:SER197
|
4.7
|
44.6
|
1.0
|
N
|
B:VAL193
|
4.8
|
43.9
|
1.0
|
O
|
B:VAL193
|
4.8
|
42.0
|
1.0
|
CA
|
B:HIS258
|
4.9
|
45.6
|
1.0
|
|
Calcium binding site 5 out
of 8 in 6qyc
Go back to
Calcium Binding Sites List in 6qyc
Calcium binding site 5 out
of 8 in the Crystal Structure of Mtrc From Shewanella Baltica OS185
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 5 of Crystal Structure of Mtrc From Shewanella Baltica OS185 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca813
b:81.9
occ:1.00
|
O
|
B:GLN511
|
2.5
|
51.8
|
1.0
|
O
|
B:HOH1063
|
2.5
|
66.2
|
1.0
|
OE1
|
B:GLU464
|
2.9
|
58.3
|
1.0
|
O
|
B:HOH1029
|
2.9
|
56.7
|
1.0
|
O
|
B:HOH1115
|
2.9
|
45.4
|
1.0
|
OE2
|
B:GLU464
|
3.5
|
59.6
|
1.0
|
CD
|
B:GLU464
|
3.6
|
56.9
|
1.0
|
C
|
B:GLN511
|
3.7
|
45.9
|
1.0
|
O
|
B:LEU465
|
4.1
|
48.5
|
1.0
|
CG
|
B:GLN511
|
4.5
|
49.4
|
1.0
|
CA
|
B:GLN511
|
4.5
|
42.5
|
1.0
|
N
|
B:VAL512
|
4.6
|
46.5
|
1.0
|
CA
|
B:VAL512
|
4.7
|
49.8
|
1.0
|
|
Calcium binding site 6 out
of 8 in 6qyc
Go back to
Calcium Binding Sites List in 6qyc
Calcium binding site 6 out
of 8 in the Crystal Structure of Mtrc From Shewanella Baltica OS185
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 6 of Crystal Structure of Mtrc From Shewanella Baltica OS185 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ca811
b:47.1
occ:1.00
|
N
|
C:GLY542
|
3.1
|
48.5
|
1.0
|
N
|
C:THR538
|
3.2
|
44.0
|
1.0
|
N
|
C:GLY546
|
3.3
|
38.8
|
1.0
|
N
|
C:ASN544
|
3.3
|
43.8
|
1.0
|
O
|
C:HOH923
|
3.3
|
41.2
|
1.0
|
CA
|
C:GLY542
|
3.5
|
45.1
|
1.0
|
OG1
|
C:THR538
|
3.5
|
44.4
|
1.0
|
C
|
C:GLY542
|
3.7
|
42.4
|
1.0
|
CA
|
C:GLY537
|
3.7
|
40.7
|
1.0
|
CA
|
C:GLY546
|
3.7
|
43.2
|
1.0
|
CB
|
C:ASN544
|
3.7
|
41.0
|
1.0
|
C
|
C:ASN544
|
3.8
|
39.2
|
1.0
|
CA
|
C:ASN544
|
3.8
|
40.6
|
1.0
|
N
|
C:LYS545
|
3.8
|
40.2
|
1.0
|
N
|
C:ALA543
|
3.8
|
45.3
|
1.0
|
N
|
C:SER541
|
3.9
|
47.3
|
1.0
|
C
|
C:GLY537
|
4.0
|
44.4
|
1.0
|
C
|
C:ALA540
|
4.1
|
44.2
|
1.0
|
CA
|
C:THR538
|
4.1
|
40.0
|
1.0
|
CB
|
C:ALA540
|
4.2
|
45.5
|
1.0
|
C
|
C:SER541
|
4.2
|
43.6
|
1.0
|
N
|
C:ALA540
|
4.2
|
42.7
|
1.0
|
O
|
C:GLY542
|
4.2
|
43.9
|
1.0
|
C
|
C:THR538
|
4.3
|
40.5
|
1.0
|
C
|
C:LYS545
|
4.3
|
42.8
|
1.0
|
O
|
C:ASN544
|
4.4
|
41.9
|
1.0
|
CA
|
C:ALA540
|
4.4
|
48.6
|
1.0
|
O
|
C:THR538
|
4.4
|
42.5
|
1.0
|
C
|
C:ALA543
|
4.4
|
43.2
|
1.0
|
CB
|
C:THR538
|
4.4
|
45.5
|
1.0
|
CA
|
C:LYS545
|
4.5
|
41.3
|
1.0
|
CA
|
C:SER541
|
4.5
|
45.7
|
1.0
|
O
|
C:ALA540
|
4.6
|
42.9
|
1.0
|
CA
|
C:ALA543
|
4.7
|
42.4
|
1.0
|
CG
|
C:ASN544
|
4.7
|
44.0
|
1.0
|
N
|
C:TYR539
|
4.9
|
42.2
|
1.0
|
O2D
|
C:HEC807
|
4.9
|
41.5
|
1.0
|
ND2
|
C:ASN544
|
4.9
|
39.7
|
1.0
|
N
|
C:GLY537
|
5.0
|
44.7
|
1.0
|
|
Calcium binding site 7 out
of 8 in 6qyc
Go back to
Calcium Binding Sites List in 6qyc
Calcium binding site 7 out
of 8 in the Crystal Structure of Mtrc From Shewanella Baltica OS185
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 7 of Crystal Structure of Mtrc From Shewanella Baltica OS185 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ca812
b:83.2
occ:1.00
|
O
|
C:HOH933
|
2.6
|
52.9
|
1.0
|
N
|
C:ALA194
|
2.7
|
54.7
|
1.0
|
OG
|
C:SER197
|
2.8
|
57.8
|
1.0
|
O
|
C:CYS257
|
2.9
|
54.2
|
1.0
|
CA
|
C:VAL193
|
3.3
|
51.9
|
1.0
|
C
|
C:VAL193
|
3.5
|
53.1
|
1.0
|
CB
|
C:SER197
|
3.5
|
50.6
|
1.0
|
CA
|
C:ALA194
|
3.6
|
58.5
|
1.0
|
O
|
C:ALA194
|
3.7
|
53.1
|
1.0
|
CB
|
C:ALA194
|
3.7
|
54.7
|
1.0
|
CB
|
C:VAL193
|
3.7
|
51.9
|
1.0
|
C
|
C:CYS257
|
4.0
|
54.7
|
1.0
|
C
|
C:ALA194
|
4.1
|
55.1
|
1.0
|
CG1
|
C:VAL193
|
4.2
|
52.2
|
1.0
|
O
|
C:ILE192
|
4.4
|
54.9
|
1.0
|
N
|
C:VAL193
|
4.6
|
53.4
|
1.0
|
O
|
C:VAL193
|
4.6
|
59.8
|
1.0
|
O
|
C:ALA259
|
4.7
|
63.2
|
1.0
|
N
|
C:ALA259
|
4.7
|
56.3
|
1.0
|
CA
|
C:CYS257
|
4.7
|
46.2
|
1.0
|
CA
|
C:SER197
|
4.8
|
55.0
|
1.0
|
N
|
C:SER197
|
4.8
|
52.2
|
1.0
|
N
|
C:HIS258
|
4.9
|
48.4
|
1.0
|
CA
|
C:HIS258
|
5.0
|
51.8
|
1.0
|
|
Calcium binding site 8 out
of 8 in 6qyc
Go back to
Calcium Binding Sites List in 6qyc
Calcium binding site 8 out
of 8 in the Crystal Structure of Mtrc From Shewanella Baltica OS185
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 8 of Crystal Structure of Mtrc From Shewanella Baltica OS185 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ca813
b:81.0
occ:1.00
|
O
|
C:GLN511
|
2.4
|
49.7
|
1.0
|
O
|
C:HOH919
|
2.5
|
52.7
|
1.0
|
O
|
C:HOH995
|
2.7
|
56.0
|
1.0
|
OE2
|
C:GLU464
|
2.8
|
54.4
|
1.0
|
O
|
C:HOH1035
|
2.9
|
46.4
|
1.0
|
OE1
|
C:GLU464
|
3.5
|
56.5
|
1.0
|
CD
|
C:GLU464
|
3.5
|
53.9
|
1.0
|
C
|
C:GLN511
|
3.6
|
50.3
|
1.0
|
O
|
C:LEU465
|
4.0
|
50.2
|
1.0
|
O
|
C:HOH1126
|
4.1
|
53.0
|
1.0
|
OE1
|
C:GLN333
|
4.3
|
69.9
|
1.0
|
CG
|
C:GLN511
|
4.4
|
49.8
|
1.0
|
CA
|
C:GLN511
|
4.5
|
48.9
|
1.0
|
N
|
C:VAL512
|
4.5
|
48.1
|
1.0
|
CA
|
C:VAL512
|
4.6
|
45.5
|
1.0
|
N
|
C:LEU465
|
4.9
|
47.7
|
1.0
|
O
|
C:MET332
|
5.0
|
54.2
|
1.0
|
|
Reference:
M.J.Edwards,
G.F.White,
J.N.Butt,
D.J.Richardson,
T.A.Clarke.
The Crystal Structure of A Biological Insulated Transmembrane Molecular Wire. Cell 2020.
ISSN: ISSN 1097-4172
PubMed: 32289252
DOI: 10.1016/J.CELL.2020.03.032
Page generated: Tue Jul 16 14:06:29 2024
|