Zinc in PDB 3h5r: Crystal Structure of E. Coli Mccb + Succinimide
Protein crystallography data
The structure of Crystal Structure of E. Coli Mccb + Succinimide, PDB code: 3h5r
was solved by
C.A.Regni,
R.F.Roush,
D.Miller,
A.Nourse,
C.T.Walsh,
B.A.Schulman,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
27.95 /
2.10
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
55.934,
137.972,
80.134,
90.00,
92.10,
90.00
|
R / Rfree (%)
|
19.4 /
25
|
Zinc Binding Sites:
The binding sites of Zinc atom in the Crystal Structure of E. Coli Mccb + Succinimide
(pdb code 3h5r). 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 E. Coli Mccb + Succinimide, PDB code: 3h5r:
Jump to Zinc binding site number:
1;
2;
3;
4;
Zinc binding site 1 out
of 4 in 3h5r
Go back to
Zinc Binding Sites List in 3h5r
Zinc binding site 1 out
of 4 in the Crystal Structure of E. Coli Mccb + Succinimide
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 E. Coli Mccb + Succinimide within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn500
b:50.6
occ:1.00
|
SG
|
A:CYS346
|
2.3
|
48.7
|
1.0
|
SG
|
A:CYS260
|
2.4
|
48.9
|
1.0
|
SG
|
A:CYS343
|
2.4
|
44.8
|
1.0
|
SG
|
A:CYS257
|
2.4
|
46.3
|
1.0
|
CB
|
A:CYS343
|
3.1
|
49.0
|
1.0
|
CB
|
A:CYS257
|
3.4
|
45.2
|
1.0
|
CB
|
A:CYS260
|
3.5
|
51.6
|
1.0
|
CB
|
A:CYS346
|
3.5
|
51.3
|
1.0
|
N
|
A:CYS346
|
3.6
|
51.7
|
1.0
|
CA
|
A:CYS260
|
3.7
|
51.5
|
1.0
|
N
|
A:CYS260
|
3.8
|
50.9
|
1.0
|
N
|
A:CYS257
|
3.9
|
46.1
|
1.0
|
CA
|
A:CYS257
|
4.1
|
46.0
|
1.0
|
CA
|
A:CYS346
|
4.1
|
51.4
|
1.0
|
C
|
A:GLU259
|
4.4
|
50.1
|
1.0
|
O
|
A:CYS257
|
4.4
|
46.0
|
1.0
|
C
|
A:CYS257
|
4.5
|
46.1
|
1.0
|
CB
|
A:VAL345
|
4.5
|
51.9
|
1.0
|
CA
|
A:CYS343
|
4.6
|
48.6
|
1.0
|
C
|
A:VAL345
|
4.7
|
51.8
|
1.0
|
C
|
A:CYS346
|
4.8
|
51.8
|
1.0
|
N
|
A:GLU259
|
4.8
|
48.5
|
1.0
|
N
|
A:VAL345
|
4.8
|
51.7
|
1.0
|
O
|
A:SER340
|
4.9
|
48.5
|
1.0
|
CA
|
A:VAL345
|
4.9
|
51.9
|
1.0
|
O
|
A:GLU259
|
4.9
|
50.0
|
1.0
|
N
|
A:GLY347
|
4.9
|
52.4
|
1.0
|
CA
|
A:GLU259
|
5.0
|
50.1
|
1.0
|
|
Zinc binding site 2 out
of 4 in 3h5r
Go back to
Zinc Binding Sites List in 3h5r
Zinc binding site 2 out
of 4 in the Crystal Structure of E. Coli Mccb + Succinimide
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 E. Coli Mccb + Succinimide within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn500
b:45.2
occ:1.00
|
SG
|
B:CYS260
|
2.2
|
46.3
|
1.0
|
SG
|
B:CYS343
|
2.2
|
53.0
|
1.0
|
SG
|
B:CYS257
|
2.4
|
47.1
|
1.0
|
SG
|
B:CYS346
|
2.5
|
50.9
|
1.0
|
CB
|
B:CYS343
|
3.1
|
52.8
|
1.0
|
CB
|
B:CYS257
|
3.3
|
46.4
|
1.0
|
CB
|
B:CYS260
|
3.5
|
53.1
|
1.0
|
N
|
B:CYS260
|
3.6
|
53.0
|
1.0
|
CA
|
B:CYS260
|
3.7
|
53.2
|
1.0
|
N
|
B:CYS257
|
3.7
|
46.6
|
1.0
|
CB
|
B:CYS346
|
3.8
|
52.8
|
1.0
|
N
|
B:CYS346
|
3.8
|
52.6
|
1.0
|
CA
|
B:CYS257
|
3.9
|
47.3
|
1.0
|
C
|
B:GLU259
|
4.2
|
52.8
|
1.0
|
CA
|
B:CYS346
|
4.2
|
52.8
|
1.0
|
C
|
B:CYS257
|
4.4
|
47.8
|
1.0
|
O
|
B:CYS257
|
4.5
|
47.5
|
1.0
|
CA
|
B:CYS343
|
4.5
|
53.2
|
1.0
|
N
|
B:GLU259
|
4.6
|
51.6
|
1.0
|
CB
|
B:GLU259
|
4.6
|
52.9
|
1.0
|
CA
|
B:GLU259
|
4.7
|
52.9
|
1.0
|
C
|
B:CYS346
|
4.7
|
53.5
|
1.0
|
O
|
B:GLU259
|
4.7
|
52.8
|
1.0
|
CB
|
B:VAL345
|
4.8
|
53.1
|
1.0
|
C
|
B:VAL345
|
4.9
|
53.0
|
1.0
|
C
|
B:GLY256
|
4.9
|
46.5
|
1.0
|
C
|
B:CYS343
|
5.0
|
53.2
|
1.0
|
|
Zinc binding site 3 out
of 4 in 3h5r
Go back to
Zinc Binding Sites List in 3h5r
Zinc binding site 3 out
of 4 in the Crystal Structure of E. Coli Mccb + Succinimide
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 E. Coli Mccb + Succinimide within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Zn500
b:37.2
occ:1.00
|
SG
|
C:CYS346
|
2.3
|
45.4
|
1.0
|
SG
|
C:CYS257
|
2.3
|
39.2
|
1.0
|
SG
|
C:CYS343
|
2.4
|
46.5
|
1.0
|
SG
|
C:CYS260
|
2.5
|
44.5
|
1.0
|
CB
|
C:CYS343
|
3.2
|
48.3
|
1.0
|
CB
|
C:CYS346
|
3.3
|
49.3
|
1.0
|
CB
|
C:CYS257
|
3.4
|
41.9
|
1.0
|
N
|
C:CYS260
|
3.6
|
47.1
|
1.0
|
CB
|
C:CYS260
|
3.6
|
47.0
|
1.0
|
N
|
C:CYS346
|
3.6
|
49.1
|
1.0
|
N
|
C:CYS257
|
3.7
|
42.9
|
1.0
|
CA
|
C:CYS260
|
3.7
|
47.8
|
1.0
|
CA
|
C:CYS257
|
4.0
|
42.4
|
1.0
|
CA
|
C:CYS346
|
4.0
|
49.7
|
1.0
|
C
|
C:GLU259
|
4.3
|
46.8
|
1.0
|
C
|
C:CYS257
|
4.4
|
43.5
|
1.0
|
O
|
C:CYS257
|
4.4
|
43.2
|
1.0
|
O
|
C:HOH378
|
4.5
|
48.5
|
1.0
|
N
|
C:GLU259
|
4.6
|
45.6
|
1.0
|
O
|
C:HOH393
|
4.7
|
37.3
|
1.0
|
CA
|
C:CYS343
|
4.7
|
48.7
|
1.0
|
CB
|
C:GLU259
|
4.7
|
47.4
|
1.0
|
C
|
C:CYS346
|
4.8
|
50.9
|
1.0
|
C
|
C:VAL345
|
4.8
|
49.4
|
1.0
|
CA
|
C:GLU259
|
4.8
|
47.2
|
1.0
|
C
|
C:GLY256
|
4.8
|
41.5
|
1.0
|
CB
|
C:VAL345
|
4.8
|
49.4
|
1.0
|
N
|
C:VAL345
|
4.9
|
49.6
|
1.0
|
O
|
C:GLU259
|
5.0
|
46.9
|
1.0
|
|
Zinc binding site 4 out
of 4 in 3h5r
Go back to
Zinc Binding Sites List in 3h5r
Zinc binding site 4 out
of 4 in the Crystal Structure of E. Coli Mccb + Succinimide
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 E. Coli Mccb + Succinimide within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Zn500
b:71.6
occ:1.00
|
SG
|
D:CYS346
|
2.3
|
56.2
|
1.0
|
SG
|
D:CYS257
|
2.6
|
53.1
|
1.0
|
SG
|
D:CYS260
|
2.7
|
55.2
|
1.0
|
SG
|
D:CYS343
|
2.8
|
55.8
|
1.0
|
CB
|
D:CYS257
|
3.3
|
52.5
|
1.0
|
CB
|
D:CYS343
|
3.5
|
55.6
|
1.0
|
N
|
D:CYS346
|
3.6
|
57.3
|
1.0
|
CB
|
D:CYS346
|
3.8
|
57.5
|
1.0
|
N
|
D:CYS257
|
3.8
|
52.3
|
1.0
|
N
|
D:CYS260
|
3.9
|
55.2
|
1.0
|
CB
|
D:CYS260
|
4.0
|
54.8
|
1.0
|
CA
|
D:CYS257
|
4.0
|
52.6
|
1.0
|
CA
|
D:CYS260
|
4.1
|
55.1
|
1.0
|
CA
|
D:CYS346
|
4.2
|
57.6
|
1.0
|
O
|
D:CYS346
|
4.2
|
58.5
|
1.0
|
O
|
D:CYS257
|
4.2
|
52.9
|
1.0
|
C
|
D:CYS257
|
4.3
|
52.9
|
1.0
|
C
|
D:GLU259
|
4.4
|
55.2
|
1.0
|
C
|
D:CYS346
|
4.6
|
58.1
|
1.0
|
CB
|
D:VAL345
|
4.7
|
56.7
|
1.0
|
C
|
D:VAL345
|
4.8
|
56.9
|
1.0
|
N
|
D:GLU259
|
4.8
|
54.8
|
1.0
|
O
|
D:GLU259
|
4.9
|
55.2
|
1.0
|
C
|
D:GLY256
|
4.9
|
51.7
|
1.0
|
CA
|
D:GLU259
|
4.9
|
55.4
|
1.0
|
CA
|
D:CYS343
|
5.0
|
55.8
|
1.0
|
|
Reference:
C.A.Regni,
R.F.Roush,
D.J.Miller,
A.Nourse,
C.T.Walsh,
B.A.Schulman.
How the Mccb Bacterial Ancestor of Ubiquitin E1 Initiates Biosynthesis of the Microcin C7 Antibiotic. Embo J. V. 28 1953 2009.
ISSN: ISSN 0261-4189
PubMed: 19494832
DOI: 10.1038/EMBOJ.2009.146
Page generated: Thu Oct 24 14:14:42 2024
|