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Sodium in PDB 3cmd: Crystal Structure of Peptide Deformylase From Vre-E.Faecium

Enzymatic activity of Crystal Structure of Peptide Deformylase From Vre-E.Faecium

All present enzymatic activity of Crystal Structure of Peptide Deformylase From Vre-E.Faecium:
3.5.1.88;

Protein crystallography data

The structure of Crystal Structure of Peptide Deformylase From Vre-E.Faecium, PDB code: 3cmd was solved by K.Y.Hwang, K.H.Nam, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.70
Space group P 64 2 2
Cell size a, b, c (Å), α, β, γ (°) 149.470, 149.470, 143.329, 90.00, 90.00, 120.00
R / Rfree (%) 20 / 22.9

Other elements in 3cmd:

The structure of Crystal Structure of Peptide Deformylase From Vre-E.Faecium also contains other interesting chemical elements:

Iron (Fe) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Peptide Deformylase From Vre-E.Faecium (pdb code 3cmd). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 8 binding sites of Sodium where determined in the Crystal Structure of Peptide Deformylase From Vre-E.Faecium, PDB code: 3cmd:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Sodium binding site 1 out of 8 in 3cmd

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Sodium binding site 1 out of 8 in the Crystal Structure of Peptide Deformylase From Vre-E.Faecium


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Peptide Deformylase From Vre-E.Faecium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na189

b:20.7
occ:1.00
 O A:HOH267 2.9 33.5 1.0
ND1 A:HIS157 3.5 13.2 1.0
O A:GLY113 3.6 22.5 1.0
CG A:HIS157 3.9 12.2 1.0
CE1 A:HIS157 3.9 10.8 1.0
N A:GLY113 3.9 23.1 1.0
CB A:GLU112 4.0 15.2 1.0
CG A:GLU112 4.1 14.4 1.0
CB A:HIS157 4.3 11.3 1.0
CD2 A:HIS157 4.4 10.2 1.0
NE2 A:HIS157 4.4 11.1 1.0
CA A:GLU112 4.4 19.6 1.0
C1 A:MLI191 4.4 28.3 1.0
OE1 A:GLU112 4.5 12.3 1.0
C A:GLY113 4.5 22.1 1.0
CD1 A:LEU108 4.6 20.8 1.0
C A:GLU112 4.6 19.5 1.0
CD A:GLU112 4.7 14.4 1.0
C3 A:MLI191 4.7 30.8 1.0
CA A:GLY113 4.7 22.0 1.0
CG2 A:VAL154 4.8 5.3 1.0
CA A:VAL154 4.8 7.9 1.0
O9 A:MLI191 5.0 30.2 1.0

Sodium binding site 2 out of 8 in 3cmd

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Sodium binding site 2 out of 8 in the Crystal Structure of Peptide Deformylase From Vre-E.Faecium


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Peptide Deformylase From Vre-E.Faecium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na190

b:22.4
occ:1.00
 O A:HOH285 2.9 30.1 1.0
OE1 A:GLU36 3.0 22.8 1.0
CD A:GLU36 3.8 19.8 1.0
CE A:MET0 3.8 26.8 1.0
OE2 A:GLU36 3.9 21.8 1.0
OD1 A:ASP6 4.2 22.9 1.0
OD2 A:ASP6 4.2 22.7 1.0
CG A:ASP6 4.2 21.2 1.0
CG1 A:ILE2 4.9 15.4 1.0
CB A:ASP6 5.0 19.3 1.0

Sodium binding site 3 out of 8 in 3cmd

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Sodium binding site 3 out of 8 in the Crystal Structure of Peptide Deformylase From Vre-E.Faecium


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of Peptide Deformylase From Vre-E.Faecium within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na189

b:23.2
occ:1.00
 OE1 B:GLU36 3.1 20.3 1.0
CD B:GLU36 4.1 20.1 1.0
OD1 B:ASP6 4.2 19.6 1.0
CG B:ASP6 4.3 18.3 1.0
OD2 B:ASP6 4.4 18.3 1.0
OE2 B:GLU36 4.4 21.5 1.0
SD B:MET0 4.5 41.8 1.0
CB B:MET0 4.6 31.3 1.0
N A:GLY182 4.7 30.9 1.0
O B:MET1 4.7 24.3 1.0
CA A:GLY182 4.8 31.1 1.0

Sodium binding site 4 out of 8 in 3cmd

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Sodium binding site 4 out of 8 in the Crystal Structure of Peptide Deformylase From Vre-E.Faecium


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of Peptide Deformylase From Vre-E.Faecium within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na190

b:32.6
occ:1.00
 CG B:GLU151 3.3 25.4 1.0
O B:HOH227 3.4 25.5 1.0
N B:GLU151 3.5 14.7 1.0
O B:LYS148 3.6 22.8 1.0
CD B:GLU151 3.8 28.3 1.0
N B:TYR150 3.9 12.1 1.0
CB B:TYR150 3.9 10.6 1.0
CB B:GLU151 3.9 20.5 1.0
OE1 B:GLU151 4.1 31.3 1.0
CB B:ASN149 4.2 38.8 1.0
CA B:TYR150 4.2 10.1 1.0
OE2 B:GLU151 4.3 30.6 1.0
CA B:GLU151 4.3 15.8 1.0
C B:TYR150 4.4 8.8 1.0
C B:ASN149 4.6 25.3 1.0
C B:LYS148 4.7 22.0 1.0
O B:HOH230 4.8 18.7 1.0
CA B:ASN149 4.9 27.0 1.0

Sodium binding site 5 out of 8 in 3cmd

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Sodium binding site 5 out of 8 in the Crystal Structure of Peptide Deformylase From Vre-E.Faecium


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Crystal Structure of Peptide Deformylase From Vre-E.Faecium within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na191

b:24.2
occ:1.00
 O8 B:MLI195 3.2 52.6 1.0
N B:GLY113 3.6 23.8 1.0
O B:GLY113 3.8 25.9 1.0
ND1 B:HIS157 4.0 6.9 1.0
C3 B:MLI195 4.0 51.1 1.0
CB B:GLU112 4.2 11.8 1.0
O9 B:MLI195 4.2 51.3 1.0
CG B:GLU112 4.3 12.0 1.0
CE1 B:HIS157 4.3 6.1 1.0
CA B:GLU112 4.3 12.4 1.0
CG B:HIS157 4.3 6.0 1.0
CD1 B:LEU108 4.4 20.1 1.0
C B:GLU112 4.4 13.0 1.0
CA B:GLY113 4.4 25.0 1.0
C B:GLY113 4.5 25.6 1.0
NE2 B:HIS157 4.7 6.6 1.0
CG2 B:VAL154 4.7 8.7 1.0
CB B:HIS157 4.7 5.5 1.0
OE1 B:GLU112 4.8 13.3 1.0
CD2 B:HIS157 4.8 5.1 1.0
CD B:GLU112 4.8 11.9 1.0
OH B:TYR150 5.0 11.5 1.0
CG2 B:VAL59 5.0 13.1 1.0

Sodium binding site 6 out of 8 in 3cmd

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Sodium binding site 6 out of 8 in the Crystal Structure of Peptide Deformylase From Vre-E.Faecium


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Crystal Structure of Peptide Deformylase From Vre-E.Faecium within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na192

b:27.1
occ:1.00
 CG B:GLU181 3.3 33.5 1.0
N B:GLU181 3.4 18.7 1.0
CB B:LYS180 3.9 39.3 1.0
CA B:LYS180 3.9 17.4 1.0
CD B:GLU181 4.1 37.0 1.0
CB B:GLU181 4.1 29.8 1.0
C B:LYS180 4.2 16.2 1.0
CG B:LYS180 4.3 43.2 1.0
CA B:GLU181 4.4 19.5 1.0
OE2 B:GLU181 4.5 39.7 1.0
CD B:LYS180 4.7 48.5 1.0
O B:HOH258 4.7 45.3 1.0
OE1 B:GLU181 4.7 38.8 1.0

Sodium binding site 7 out of 8 in 3cmd

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Sodium binding site 7 out of 8 in the Crystal Structure of Peptide Deformylase From Vre-E.Faecium


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Crystal Structure of Peptide Deformylase From Vre-E.Faecium within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na193

b:23.7
occ:1.00
 OH B:TYR168 3.4 27.0 1.0
OE1 B:GLU10 3.5 20.8 1.0
CG B:GLU10 4.0 21.1 1.0
NE B:ARG16 4.1 26.3 1.0
O B:HOH215 4.1 27.2 1.0
NH2 B:ARG16 4.1 24.9 1.0
CD B:GLU10 4.2 20.2 1.0
CZ B:TYR168 4.3 26.0 1.0
CE1 B:TYR168 4.4 26.6 1.0
CZ B:ARG16 4.6 25.6 1.0
N B:GLY11 4.8 19.9 1.0

Sodium binding site 8 out of 8 in 3cmd

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Sodium binding site 8 out of 8 in the Crystal Structure of Peptide Deformylase From Vre-E.Faecium


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Crystal Structure of Peptide Deformylase From Vre-E.Faecium within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na194

b:16.0
occ:1.00
 O B:HIS101 3.0 13.9 1.0
OG B:SER100 3.1 25.8 1.0
C B:HIS101 3.3 14.2 1.0
NH2 B:ARG146 3.4 19.1 1.0
N B:SER102 3.7 16.1 1.0
CA B:SER102 3.8 14.2 1.0
N B:HIS101 4.1 16.5 1.0
CA B:HIS101 4.2 15.7 1.0
NH1 B:ARG146 4.2 17.9 1.0
CZ B:ARG146 4.2 18.9 1.0
CB B:SER100 4.5 21.0 1.0
O B:HOH240 4.6 24.8 1.0
CB B:SER102 4.7 10.4 1.0
C B:SER100 4.8 16.7 1.0
O B:HOH256 4.8 36.7 1.0
C B:SER102 5.0 14.1 1.0

Reference:

K.H.Nam, J.I.Ham, A.Priyadarshi, E.E.Kim, N.Chung, K.Y.Hwang. Insight Into the Antibacterial Drug Design and Architectural Mechanism of Peptide Recognition From the E. Faecium Peptide Deformylase Structure. Proteins V. 74 261 2009.
ISSN: ISSN 0887-3585
PubMed: 18831047
DOI: 10.1002/PROT.22257
Page generated: Mon Oct 7 07:13:44 2024

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