Zinc in PDB 6cmk: Crystal Structure of Citrobacter Koseri Aztd
Protein crystallography data
The structure of Crystal Structure of Citrobacter Koseri Aztd, PDB code: 6cmk
was solved by
E.T.Yukl,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
64.40 /
1.73
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
54.230,
128.790,
56.850,
90.00,
105.20,
90.00
|
R / Rfree (%)
|
15.3 /
18.8
|
Zinc Binding Sites:
The binding sites of Zinc atom in the Crystal Structure of Citrobacter Koseri Aztd
(pdb code 6cmk). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the
Crystal Structure of Citrobacter Koseri Aztd, PDB code: 6cmk:
Jump to Zinc binding site number:
1;
2;
3;
4;
Zinc binding site 1 out
of 4 in 6cmk
Go back to
Zinc Binding Sites List in 6cmk
Zinc binding site 1 out
of 4 in the Crystal Structure of Citrobacter Koseri Aztd
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 1 of Crystal Structure of Citrobacter Koseri Aztd within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn502
b:64.8
occ:0.92
|
OD1
|
B:ASP106
|
2.2
|
83.6
|
1.0
|
OD2
|
B:ASP106
|
2.8
|
83.3
|
1.0
|
NE2
|
B:HIS101
|
2.8
|
86.2
|
1.0
|
CE1
|
B:HIS405
|
2.8
|
81.8
|
1.0
|
NE2
|
B:HIS104
|
2.8
|
42.2
|
0.5
|
CG
|
B:ASP106
|
2.8
|
79.7
|
1.0
|
NE2
|
B:HIS405
|
2.8
|
83.6
|
1.0
|
CE1
|
B:HIS104
|
3.0
|
41.6
|
0.5
|
CE1
|
B:HIS101
|
3.0
|
88.1
|
1.0
|
HB3
|
B:LYS403
|
3.6
|
55.7
|
1.0
|
CD2
|
B:HIS101
|
3.6
|
85.1
|
1.0
|
ND1
|
B:HIS101
|
3.9
|
87.7
|
1.0
|
CD2
|
B:HIS104
|
4.0
|
42.5
|
0.5
|
ND1
|
B:HIS405
|
4.0
|
85.4
|
1.0
|
HB2
|
B:LYS403
|
4.1
|
55.7
|
1.0
|
ND1
|
B:HIS104
|
4.1
|
39.8
|
0.5
|
CD2
|
B:HIS405
|
4.1
|
86.7
|
1.0
|
CG
|
B:HIS101
|
4.3
|
84.4
|
1.0
|
CB
|
B:ASP106
|
4.3
|
54.5
|
1.0
|
CB
|
B:LYS403
|
4.3
|
46.4
|
1.0
|
O
|
B:VAL404
|
4.6
|
93.8
|
1.0
|
HA
|
B:ASP106
|
4.6
|
50.9
|
1.0
|
CG
|
B:HIS104
|
4.7
|
54.2
|
0.5
|
HB2
|
B:ASP106
|
4.7
|
65.5
|
1.0
|
CG
|
B:HIS405
|
4.7
|
91.4
|
1.0
|
HB3
|
B:ASP106
|
4.7
|
65.5
|
1.0
|
HG2
|
B:LYS403
|
4.9
|
71.0
|
1.0
|
CA
|
B:ASP106
|
4.9
|
42.4
|
1.0
|
N
|
B:ASP106
|
5.0
|
38.8
|
1.0
|
|
Zinc binding site 2 out
of 4 in 6cmk
Go back to
Zinc Binding Sites List in 6cmk
Zinc binding site 2 out
of 4 in the Crystal Structure of Citrobacter Koseri Aztd
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 2 of Crystal Structure of Citrobacter Koseri Aztd within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn503
b:23.4
occ:0.69
|
HE1
|
A:HIS104
|
1.7
|
51.9
|
0.5
|
HE1
|
A:HIS104
|
1.8
|
51.2
|
0.5
|
NE2
|
B:HIS126
|
2.0
|
30.4
|
1.0
|
NE2
|
B:HIS216
|
2.0
|
19.4
|
1.0
|
NE2
|
B:HIS169
|
2.2
|
28.3
|
1.0
|
CE1
|
A:HIS104
|
2.5
|
42.6
|
0.5
|
HE2
|
A:HIS104
|
2.5
|
53.7
|
0.5
|
CE1
|
A:HIS104
|
2.5
|
43.3
|
0.5
|
NE2
|
A:HIS104
|
2.8
|
44.7
|
0.5
|
HE2
|
A:HIS104
|
2.8
|
53.7
|
0.5
|
CE1
|
B:HIS169
|
2.9
|
23.1
|
1.0
|
CE1
|
B:HIS126
|
3.0
|
32.2
|
1.0
|
HE1
|
B:HIS169
|
3.0
|
27.7
|
1.0
|
NE2
|
A:HIS104
|
3.0
|
44.8
|
0.5
|
CD2
|
B:HIS126
|
3.0
|
32.3
|
1.0
|
CE1
|
B:HIS216
|
3.0
|
19.3
|
1.0
|
CD2
|
B:HIS216
|
3.0
|
18.7
|
1.0
|
HE1
|
B:HIS126
|
3.1
|
38.6
|
1.0
|
HE1
|
B:HIS216
|
3.2
|
23.1
|
1.0
|
HD2
|
B:HIS126
|
3.2
|
38.8
|
1.0
|
HD2
|
B:HIS216
|
3.2
|
22.4
|
1.0
|
CD2
|
B:HIS169
|
3.4
|
29.1
|
1.0
|
HB3
|
A:HIS101
|
3.4
|
23.5
|
1.0
|
HD2
|
B:HIS169
|
3.7
|
34.9
|
1.0
|
ND1
|
A:HIS104
|
3.7
|
41.2
|
0.5
|
ND1
|
A:HIS104
|
3.7
|
40.6
|
0.5
|
O
|
B:HOH781
|
4.0
|
25.9
|
1.0
|
ND1
|
B:HIS126
|
4.1
|
34.9
|
1.0
|
CD2
|
A:HIS104
|
4.1
|
43.9
|
0.5
|
CG
|
B:HIS126
|
4.1
|
25.8
|
1.0
|
ND1
|
B:HIS216
|
4.1
|
15.7
|
1.0
|
ND1
|
B:HIS169
|
4.2
|
27.7
|
1.0
|
CG
|
B:HIS216
|
4.2
|
12.9
|
1.0
|
CD2
|
A:HIS104
|
4.3
|
43.6
|
0.5
|
CB
|
A:HIS101
|
4.4
|
19.6
|
1.0
|
CG
|
B:HIS169
|
4.4
|
27.2
|
1.0
|
O
|
A:HIS101
|
4.4
|
27.9
|
1.0
|
ZN
|
A:ZN502
|
4.4
|
37.8
|
0.6
|
ND1
|
A:HIS101
|
4.6
|
24.4
|
1.0
|
CG
|
A:HIS104
|
4.6
|
41.9
|
0.5
|
CG
|
A:HIS104
|
4.7
|
41.9
|
0.5
|
CG
|
A:HIS101
|
4.7
|
20.5
|
1.0
|
HB2
|
A:HIS101
|
4.7
|
23.5
|
1.0
|
O
|
B:HOH738
|
4.7
|
23.6
|
1.0
|
O2S
|
B:MES501
|
4.8
|
28.9
|
1.0
|
HD2
|
A:HIS104
|
4.8
|
52.6
|
0.5
|
OD2
|
A:ASP103
|
4.8
|
86.2
|
1.0
|
HD1
|
B:HIS126
|
4.8
|
41.9
|
1.0
|
HD1
|
B:HIS169
|
4.9
|
33.2
|
1.0
|
HD1
|
B:HIS216
|
4.9
|
18.8
|
1.0
|
|
Zinc binding site 3 out
of 4 in 6cmk
Go back to
Zinc Binding Sites List in 6cmk
Zinc binding site 3 out
of 4 in the Crystal Structure of Citrobacter Koseri Aztd
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 3 of Crystal Structure of Citrobacter Koseri Aztd within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn502
b:37.8
occ:0.64
|
HE2
|
A:HIS104
|
1.9
|
53.7
|
0.5
|
OD1
|
A:ASP106
|
2.2
|
32.1
|
1.0
|
HE2
|
A:HIS104
|
2.2
|
53.7
|
0.5
|
HD2
|
A:HIS104
|
2.3
|
52.6
|
0.5
|
HD2
|
A:HIS104
|
2.4
|
52.4
|
0.5
|
NE2
|
A:HIS104
|
2.5
|
44.8
|
0.5
|
ND1
|
A:HIS101
|
2.6
|
24.4
|
1.0
|
NE2
|
A:HIS104
|
2.7
|
44.7
|
0.5
|
CD2
|
A:HIS104
|
2.7
|
43.6
|
0.5
|
CD2
|
A:HIS104
|
2.8
|
43.9
|
0.5
|
CG
|
A:ASP106
|
2.8
|
36.1
|
1.0
|
OD2
|
A:ASP106
|
2.8
|
34.5
|
1.0
|
NE2
|
A:HIS405
|
2.9
|
35.2
|
1.0
|
CE1
|
A:HIS101
|
3.4
|
25.5
|
1.0
|
HE1
|
A:HIS101
|
3.4
|
30.6
|
1.0
|
HD2
|
B:HIS169
|
3.5
|
34.9
|
1.0
|
CD2
|
B:HIS169
|
3.6
|
29.1
|
1.0
|
CE1
|
A:HIS405
|
3.6
|
25.9
|
1.0
|
NE2
|
B:HIS169
|
3.6
|
28.3
|
1.0
|
CG
|
A:HIS101
|
3.7
|
20.5
|
1.0
|
HB2
|
A:HIS101
|
3.7
|
23.5
|
1.0
|
CE1
|
A:HIS104
|
3.7
|
43.3
|
0.5
|
HB3
|
A:HIS101
|
3.9
|
23.5
|
1.0
|
CE1
|
A:HIS104
|
4.0
|
42.6
|
0.5
|
CB
|
A:HIS101
|
4.0
|
19.6
|
1.0
|
CD2
|
A:HIS405
|
4.0
|
35.6
|
1.0
|
CG
|
A:HIS104
|
4.1
|
41.9
|
0.5
|
CG
|
A:HIS104
|
4.1
|
41.9
|
0.5
|
CB
|
A:ASP106
|
4.2
|
26.0
|
1.0
|
HE1
|
A:HIS104
|
4.2
|
51.9
|
0.5
|
CG
|
B:HIS169
|
4.2
|
27.2
|
1.0
|
CE1
|
B:HIS169
|
4.3
|
23.1
|
1.0
|
ZN
|
B:ZN503
|
4.4
|
23.4
|
0.7
|
HB2
|
A:LYS403
|
4.4
|
25.5
|
1.0
|
HD2
|
B:HIS216
|
4.5
|
22.4
|
1.0
|
HB2
|
A:ASP106
|
4.5
|
31.2
|
1.0
|
ND1
|
A:HIS104
|
4.5
|
41.2
|
0.5
|
HE1
|
A:HIS104
|
4.5
|
51.2
|
0.5
|
NE2
|
B:HIS216
|
4.6
|
19.4
|
1.0
|
NE2
|
A:HIS101
|
4.6
|
27.2
|
1.0
|
N
|
A:ASP106
|
4.6
|
17.0
|
1.0
|
ND1
|
B:HIS169
|
4.6
|
27.7
|
1.0
|
CD2
|
B:HIS216
|
4.7
|
18.7
|
1.0
|
ND1
|
A:HIS104
|
4.7
|
40.6
|
0.5
|
H
|
A:ASP106
|
4.7
|
20.4
|
1.0
|
CD2
|
A:HIS101
|
4.7
|
22.9
|
1.0
|
HA
|
A:ASP106
|
4.8
|
20.6
|
1.0
|
HE1
|
B:HIS169
|
4.8
|
27.7
|
1.0
|
CA
|
A:ASP106
|
4.8
|
17.2
|
1.0
|
HD2
|
A:LYS403
|
4.8
|
57.1
|
1.0
|
ND1
|
A:HIS405
|
4.8
|
33.5
|
1.0
|
HB3
|
A:ASP106
|
4.8
|
31.2
|
1.0
|
HB3
|
B:HIS169
|
4.9
|
41.7
|
1.0
|
C
|
A:ALA105
|
4.9
|
17.9
|
1.0
|
|
Zinc binding site 4 out
of 4 in 6cmk
Go back to
Zinc Binding Sites List in 6cmk
Zinc binding site 4 out
of 4 in the Crystal Structure of Citrobacter Koseri Aztd
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 4 of Crystal Structure of Citrobacter Koseri Aztd within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn503
b:36.2
occ:0.44
|
HE2
|
A:HIS126
|
1.5
|
61.8
|
1.0
|
HE2
|
A:HIS216
|
1.7
|
67.9
|
1.0
|
NE2
|
A:HIS169
|
2.2
|
36.2
|
1.0
|
NE2
|
A:HIS126
|
2.4
|
51.5
|
1.0
|
NE2
|
A:HIS216
|
2.4
|
56.5
|
1.0
|
CE1
|
A:HIS169
|
2.9
|
36.3
|
1.0
|
HE1
|
A:HIS169
|
2.9
|
43.6
|
1.0
|
CE1
|
A:HIS216
|
3.2
|
52.6
|
1.0
|
CD2
|
A:HIS126
|
3.3
|
54.3
|
1.0
|
CE1
|
A:HIS126
|
3.3
|
55.5
|
1.0
|
HE1
|
A:HIS216
|
3.3
|
63.1
|
1.0
|
CD2
|
A:HIS169
|
3.3
|
38.8
|
1.0
|
CD2
|
A:HIS216
|
3.4
|
58.6
|
1.0
|
HD2
|
A:HIS126
|
3.5
|
65.2
|
1.0
|
HE1
|
A:HIS126
|
3.5
|
66.7
|
1.0
|
HD2
|
A:HIS216
|
3.6
|
70.4
|
1.0
|
HD2
|
A:HIS169
|
3.7
|
46.6
|
1.0
|
ND1
|
A:HIS169
|
4.1
|
30.7
|
1.0
|
O
|
A:HOH887
|
4.3
|
48.5
|
1.0
|
ND1
|
A:HIS216
|
4.3
|
49.2
|
1.0
|
CG
|
A:HIS169
|
4.4
|
28.8
|
1.0
|
ND1
|
A:HIS126
|
4.4
|
52.1
|
1.0
|
CG
|
A:HIS216
|
4.5
|
45.8
|
1.0
|
CG
|
A:HIS126
|
4.5
|
46.0
|
1.0
|
HD1
|
A:HIS169
|
4.8
|
36.9
|
1.0
|
HH21
|
A:ARG192
|
4.9
|
39.3
|
0.4
|
|
Reference:
D.P.Neupane,
S.H.Fullam,
K.N.Chacon,
E.T.Yukl.
Crystal Structures of Aztd Provide Mechanistic Insights Into Direct Zinc Transfer Between Proteins. Commun Biol V. 2 308 2019.
ISSN: ESSN 2399-3642
PubMed: 31428696
DOI: 10.1038/S42003-019-0542-Z
Page generated: Mon Oct 28 19:00:46 2024
|