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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: Wed Dec 16 04:23:01 2020

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