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Zinc in PDB 3h5n: Crystal Structure of E. Coli Mccb + Atp

Protein crystallography data

The structure of Crystal Structure of E. Coli Mccb + Atp, PDB code: 3h5n 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) 42.64 / 1.90
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 55.847, 138.239, 80.224, 90.00, 92.62, 90.00
R / Rfree (%) 20.4 / 25.6

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of E. Coli Mccb + Atp (pdb code 3h5n). 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 + Atp, PDB code: 3h5n:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 3h5n

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Zinc binding site 1 out of 4 in the Crystal Structure of E. Coli Mccb + Atp


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 + Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn500

b:33.5
occ:1.00
SG A:CYS343 2.3 40.5 1.0
SG A:CYS346 2.3 35.9 1.0
SG A:CYS260 2.3 33.9 1.0
SG A:CYS257 2.4 28.6 1.0
CB A:CYS343 3.0 40.9 1.0
CB A:CYS260 3.5 36.3 1.0
CB A:CYS257 3.5 29.4 1.0
CB A:CYS346 3.6 38.3 1.0
CA A:CYS260 3.6 36.4 1.0
N A:CYS260 3.6 36.1 1.0
N A:CYS257 3.8 29.7 1.0
N A:CYS346 3.8 38.7 1.0
CA A:CYS257 4.1 29.8 1.0
CA A:CYS346 4.2 38.4 1.0
C A:GLU259 4.3 35.4 1.0
C A:CYS257 4.4 30.2 1.0
O A:CYS257 4.5 29.8 1.0
CA A:CYS343 4.5 40.8 1.0
C A:CYS346 4.7 39.0 1.0
CB A:VAL345 4.7 39.3 1.0
N A:GLY347 4.8 39.5 1.0
N A:GLU259 4.8 33.5 1.0
C A:VAL345 4.9 39.1 1.0
O A:SER340 4.9 40.4 1.0
O A:GLU259 5.0 35.6 1.0
N A:VAL345 5.0 39.9 1.0
CA A:GLU259 5.0 34.9 1.0
C A:GLY256 5.0 29.6 1.0

Zinc binding site 2 out of 4 in 3h5n

Go back to Zinc Binding Sites List in 3h5n
Zinc binding site 2 out of 4 in the Crystal Structure of E. Coli Mccb + Atp


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 + Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn500

b:24.4
occ:1.00
SG B:CYS260 2.2 23.0 1.0
SG B:CYS346 2.3 26.3 1.0
SG B:CYS257 2.3 21.5 1.0
SG B:CYS343 2.4 27.9 1.0
CB B:CYS257 3.2 22.2 1.0
CB B:CYS343 3.3 31.0 1.0
CB B:CYS260 3.5 26.1 1.0
CB B:CYS346 3.5 28.4 1.0
N B:CYS260 3.5 25.8 1.0
N B:CYS257 3.6 22.4 1.0
CA B:CYS260 3.6 26.6 1.0
N B:CYS346 3.8 28.4 1.0
CA B:CYS257 3.9 22.3 1.0
CA B:CYS346 4.2 28.7 1.0
C B:GLU259 4.3 25.5 1.0
C B:CYS257 4.3 22.3 1.0
O B:CYS257 4.4 22.7 1.0
N B:GLU259 4.7 24.3 1.0
O B:HOH373 4.7 18.4 1.0
C B:CYS346 4.7 29.7 1.0
CA B:CYS343 4.7 31.1 1.0
CB B:VAL345 4.8 28.6 1.0
CB B:GLU259 4.8 25.8 1.0
N B:GLY347 4.8 30.7 1.0
C B:GLY256 4.8 22.3 1.0
CA B:GLU259 4.8 25.6 1.0
C B:VAL345 4.9 28.6 1.0

Zinc binding site 3 out of 4 in 3h5n

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Zinc binding site 3 out of 4 in the Crystal Structure of E. Coli Mccb + Atp


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 + Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn500

b:20.1
occ:1.00
SG C:CYS346 2.2 23.4 1.0
SG C:CYS257 2.3 21.8 1.0
SG C:CYS343 2.3 23.4 1.0
SG C:CYS260 2.4 23.6 1.0
CB C:CYS343 3.2 26.1 1.0
CB C:CYS346 3.3 28.4 1.0
CB C:CYS257 3.4 19.3 1.0
N C:CYS260 3.5 27.4 1.0
CB C:CYS260 3.5 28.0 1.0
CA C:CYS260 3.6 28.4 1.0
N C:CYS257 3.7 19.0 1.0
N C:CYS346 3.8 28.3 1.0
CA C:CYS257 4.0 19.3 1.0
CA C:CYS346 4.1 28.7 1.0
C C:GLU259 4.2 26.4 1.0
O C:CYS257 4.3 19.1 1.0
C C:CYS257 4.3 19.6 1.0
CA C:CYS343 4.6 26.3 1.0
N C:GLU259 4.7 23.9 1.0
O C:HOH600 4.7 30.3 1.0
C C:GLY256 4.8 18.6 1.0
CA C:GLU259 4.8 25.9 1.0
O C:HOH400 4.8 29.5 1.0
CB C:GLU259 4.8 26.3 1.0
O C:GLU259 4.9 26.4 1.0
C C:CYS346 4.9 30.2 1.0
C C:VAL345 4.9 27.9 1.0
CB C:VAL345 5.0 28.2 1.0

Zinc binding site 4 out of 4 in 3h5n

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Zinc binding site 4 out of 4 in the Crystal Structure of E. Coli Mccb + Atp


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 + Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn500

b:33.3
occ:1.00
SG D:CYS346 2.1 33.2 1.0
SG D:CYS343 2.3 37.5 1.0
SG D:CYS257 2.4 28.2 1.0
SG D:CYS260 2.5 31.7 1.0
CB D:CYS343 3.2 38.4 1.0
CB D:CYS257 3.4 29.4 1.0
CB D:CYS346 3.5 35.4 1.0
N D:CYS260 3.5 33.4 1.0
CB D:CYS260 3.6 33.3 1.0
CA D:CYS260 3.7 33.6 1.0
N D:CYS346 3.8 35.8 1.0
N D:CYS257 3.8 29.4 1.0
CA D:CYS257 4.0 29.3 1.0
CA D:CYS346 4.1 35.8 1.0
C D:GLU259 4.3 33.6 1.0
CB D:GLU259 4.4 34.1 1.0
C D:CYS257 4.4 29.7 1.0
O D:CYS257 4.5 29.2 1.0
O D:CYS346 4.5 37.1 1.0
CA D:CYS343 4.6 38.4 1.0
C D:CYS346 4.7 36.5 1.0
N D:GLU259 4.7 32.5 1.0
CA D:GLU259 4.7 33.7 1.0
O D:HOH370 4.8 24.4 1.0
CB D:VAL345 4.8 36.4 1.0
C D:VAL345 4.9 36.1 1.0
N D:VAL345 4.9 37.0 1.0
C D:GLY256 4.9 29.3 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: Sat Sep 26 10:30:36 2020
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