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Zinc in PDB 3czx: The Crystal Structure of the Putative N-Acetylmuramoyl-L- Alanine Amidase From Neisseria Meningitidis

Protein crystallography data

The structure of The Crystal Structure of the Putative N-Acetylmuramoyl-L- Alanine Amidase From Neisseria Meningitidis, PDB code: 3czx was solved by R.Zhang, M.Zhou, M.Bargassa, A.Joachimiak, Midwest Center Forstructural Genomics (Mcsg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 74.74 / 1.60
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 67.955, 65.039, 79.319, 90.00, 109.53, 90.00
R / Rfree (%) 18 / 21.8

Zinc Binding Sites:

The binding sites of Zinc atom in the The Crystal Structure of the Putative N-Acetylmuramoyl-L- Alanine Amidase From Neisseria Meningitidis (pdb code 3czx). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the The Crystal Structure of the Putative N-Acetylmuramoyl-L- Alanine Amidase From Neisseria Meningitidis, PDB code: 3czx:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 3czx

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Zinc binding site 1 out of 4 in the The Crystal Structure of the Putative N-Acetylmuramoyl-L- Alanine Amidase From Neisseria Meningitidis


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of The Crystal Structure of the Putative N-Acetylmuramoyl-L- Alanine Amidase From Neisseria Meningitidis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:27.4
occ:1.00
OE2 A:GLU25 2.1 14.0 1.0
NE2 A:HIS11 2.2 19.7 1.0
ND1 A:HIS77 2.2 16.8 1.0
O A:HOH337 2.2 20.6 1.0
O A:HOH353 2.3 25.1 1.0
CD A:GLU25 3.0 14.6 1.0
CE1 A:HIS77 3.0 18.1 1.0
CD2 A:HIS11 3.1 18.5 1.0
CE1 A:HIS11 3.2 21.7 1.0
OE1 A:GLU25 3.2 14.7 1.0
CG A:HIS77 3.3 13.8 1.0
CB A:HIS77 3.7 11.6 1.0
NE2 A:HIS130 3.9 21.3 1.0
CE1 A:HIS130 4.1 21.9 1.0
O A:THR78 4.1 15.8 1.0
NE2 A:HIS77 4.2 15.0 1.0
CG A:GLU25 4.3 10.1 1.0
CG A:HIS11 4.3 20.2 1.0
ND1 A:HIS11 4.3 23.4 1.0
CD2 A:HIS77 4.4 14.6 1.0
CA A:HIS77 4.5 10.6 1.0
OG A:SER131 4.6 29.1 1.0
N A:THR78 4.6 10.4 1.0

Zinc binding site 2 out of 4 in 3czx

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Zinc binding site 2 out of 4 in the The Crystal Structure of the Putative N-Acetylmuramoyl-L- Alanine Amidase From Neisseria Meningitidis


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of The Crystal Structure of the Putative N-Acetylmuramoyl-L- Alanine Amidase From Neisseria Meningitidis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn301

b:18.3
occ:1.00
OE2 B:GLU25 2.1 9.4 1.0
NE2 B:HIS11 2.2 11.6 1.0
O B:HOH685 2.2 22.3 1.0
ND1 B:HIS77 2.3 9.3 1.0
O B:HOH496 2.3 20.5 1.0
CD B:GLU25 2.9 7.9 1.0
CD2 B:HIS11 3.2 11.9 1.0
CE1 B:HIS77 3.2 11.4 1.0
CE1 B:HIS11 3.2 12.1 1.0
OE1 B:GLU25 3.2 12.4 1.0
CG B:HIS77 3.4 9.1 1.0
CB B:HIS77 3.7 10.0 1.0
NE2 B:HIS130 3.9 18.4 1.0
CE1 B:HIS130 4.0 16.2 1.0
O B:THR78 4.2 13.5 1.0
CG B:GLU25 4.2 7.4 1.0
ND1 B:HIS11 4.3 11.5 1.0
CG B:HIS11 4.3 8.8 1.0
NE2 B:HIS77 4.4 9.4 1.0
O B:HOH574 4.4 28.3 1.0
CD2 B:HIS77 4.4 8.3 1.0
CA B:HIS77 4.5 8.4 1.0
OG B:SER131 4.5 19.1 1.0
N B:THR78 4.6 9.1 1.0

Zinc binding site 3 out of 4 in 3czx

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Zinc binding site 3 out of 4 in the The Crystal Structure of the Putative N-Acetylmuramoyl-L- Alanine Amidase From Neisseria Meningitidis


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of The Crystal Structure of the Putative N-Acetylmuramoyl-L- Alanine Amidase From Neisseria Meningitidis within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn301

b:19.8
occ:1.00
O C:HOH390 2.1 21.2 1.0
OE2 C:GLU25 2.2 11.6 1.0
NE2 C:HIS11 2.2 12.9 1.0
ND1 C:HIS77 2.2 11.5 1.0
CD C:GLU25 3.0 10.8 1.0
CD2 C:HIS11 3.1 12.6 1.0
CE1 C:HIS77 3.2 10.5 1.0
CE1 C:HIS11 3.2 14.7 1.0
CG C:HIS77 3.3 9.6 1.0
OE1 C:GLU25 3.3 13.6 1.0
CB C:HIS77 3.6 11.1 1.0
O C:HOH361 3.6 32.0 1.0
NE2 C:HIS130 4.0 19.9 1.0
CE1 C:HIS130 4.0 19.9 1.0
O C:THR78 4.2 14.6 1.0
O C:HOH512 4.3 29.4 1.0
NE2 C:HIS77 4.3 9.5 1.0
CG C:HIS11 4.3 10.5 1.0
ND1 C:HIS11 4.3 14.2 1.0
CG C:GLU25 4.3 8.9 1.0
CD2 C:HIS77 4.4 10.4 1.0
OG C:SER131 4.4 21.1 1.0
CA C:HIS77 4.5 9.8 1.0
N C:THR78 4.6 10.5 1.0
OE1 C:GLU144 4.9 25.5 1.0

Zinc binding site 4 out of 4 in 3czx

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Zinc binding site 4 out of 4 in the The Crystal Structure of the Putative N-Acetylmuramoyl-L- Alanine Amidase From Neisseria Meningitidis


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of The Crystal Structure of the Putative N-Acetylmuramoyl-L- Alanine Amidase From Neisseria Meningitidis within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn301

b:30.0
occ:1.00
OE2 D:GLU25 2.2 12.9 1.0
NE2 D:HIS11 2.2 20.4 1.0
ND1 D:HIS77 2.3 15.3 1.0
O D:HOH627 2.4 27.5 1.0
CD D:GLU25 2.9 16.0 1.0
CD2 D:HIS11 3.0 18.9 1.0
CE1 D:HIS77 3.1 16.1 1.0
OE1 D:GLU25 3.2 13.2 1.0
CE1 D:HIS11 3.3 21.1 1.0
CG D:HIS77 3.4 14.7 1.0
CB D:HIS77 3.8 12.3 1.0
NE2 D:HIS130 3.8 32.1 1.0
CE1 D:HIS130 4.1 32.7 1.0
CG D:HIS11 4.2 18.9 1.0
O D:THR78 4.2 16.2 1.0
CG D:GLU25 4.2 13.5 1.0
O D:HOH632 4.3 26.9 1.0
NE2 D:HIS77 4.3 16.1 1.0
ND1 D:HIS11 4.3 19.3 1.0
OG D:SER131 4.4 32.7 1.0
CD2 D:HIS77 4.5 11.7 1.0
CA D:HIS77 4.6 12.5 1.0
N D:THR78 4.8 13.0 1.0
CD2 D:HIS130 4.9 32.1 1.0

Reference:

R.Zhang, M.Zhou, M.Bargassa, A.Joachimiak. The Crystal Structure of the Putative N-Acetylmuramoyl-L-Alanine Amidase From Neisseria Meningitidis. To Be Published.
Page generated: Wed Dec 16 04:11:40 2020

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