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Magnesium in PDB 7vrd: Crystal Structure of ENOLASE1 From Candida Albicans Complexed with 2'- Phosphoglyceric Acid Sodium

Enzymatic activity of Crystal Structure of ENOLASE1 From Candida Albicans Complexed with 2'- Phosphoglyceric Acid Sodium

All present enzymatic activity of Crystal Structure of ENOLASE1 From Candida Albicans Complexed with 2'- Phosphoglyceric Acid Sodium:
4.2.1.11;

Protein crystallography data

The structure of Crystal Structure of ENOLASE1 From Candida Albicans Complexed with 2'- Phosphoglyceric Acid Sodium, PDB code: 7vrd was solved by M.Zhang, X.Zhang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.06 / 1.70
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 264.264, 61.848, 111.752, 90, 109.8, 90
R / Rfree (%) 17.2 / 19.7

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of ENOLASE1 From Candida Albicans Complexed with 2'- Phosphoglyceric Acid Sodium (pdb code 7vrd). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Crystal Structure of ENOLASE1 From Candida Albicans Complexed with 2'- Phosphoglyceric Acid Sodium, PDB code: 7vrd:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 7vrd

Go back to Magnesium Binding Sites List in 7vrd
Magnesium binding site 1 out of 6 in the Crystal Structure of ENOLASE1 From Candida Albicans Complexed with 2'- Phosphoglyceric Acid Sodium


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of ENOLASE1 From Candida Albicans Complexed with 2'- Phosphoglyceric Acid Sodium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg501

b:9.6
occ:1.00
 O A:HOH674 2.0 10.1 1.0
O4P A:2PG503 2.0 10.8 1.0
O A:SER41 2.0 10.2 1.0
O A:HOH613 2.1 8.8 1.0
OG A:SER41 2.2 9.6 1.0
O1 A:2PG503 2.2 13.3 1.0
C A:SER41 3.0 10.7 1.0
CB A:SER41 3.1 10.2 1.0
C1 A:2PG503 3.1 15.4 1.0
P A:2PG503 3.3 11.2 1.0
CA A:SER41 3.5 10.4 1.0
O1P A:2PG503 3.6 13.5 1.0
C2 A:2PG503 3.6 15.0 1.0
OD2 A:ASP324 3.8 9.9 1.0
O2P A:2PG503 3.9 10.8 1.0
NZ A:LYS349 3.9 14.2 1.0
MG A:MG502 4.0 9.9 1.0
OD1 A:ASP325 4.1 11.1 1.0
N A:SER41 4.1 10.7 1.0
NH2 A:ARG378 4.1 9.0 1.0
OD2 A:ASP325 4.1 11.6 1.0
O2 A:2PG503 4.2 15.2 1.0
O A:HOH628 4.2 9.6 1.0
N A:THR42 4.2 11.0 1.0
NE2 A:GLN169 4.3 10.2 1.0
OE1 A:GLN169 4.3 10.7 1.0
O3P A:2PG503 4.5 10.9 1.0
CG A:ASP325 4.5 10.7 1.0
CA A:THR42 4.7 11.3 1.0
CD A:GLN169 4.8 10.2 1.0
CG A:ASP324 4.9 9.5 1.0

Magnesium binding site 2 out of 6 in 7vrd

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Magnesium binding site 2 out of 6 in the Crystal Structure of ENOLASE1 From Candida Albicans Complexed with 2'- Phosphoglyceric Acid Sodium


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of ENOLASE1 From Candida Albicans Complexed with 2'- Phosphoglyceric Acid Sodium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg502

b:9.9
occ:1.00
 OE2 A:GLU297 2.0 10.7 1.0
O A:HOH628 2.1 9.6 1.0
OD2 A:ASP324 2.1 9.9 1.0
OD2 A:ASP248 2.1 10.7 1.0
O2 A:2PG503 2.1 15.2 1.0
O1 A:2PG503 2.3 13.3 1.0
C1 A:2PG503 2.5 15.4 1.0
CG A:ASP248 3.0 10.2 1.0
CG A:ASP324 3.1 9.5 1.0
CD A:GLU297 3.1 10.3 1.0
OD1 A:ASP248 3.3 10.2 1.0
CB A:ASP324 3.6 9.3 1.0
O A:HOH613 3.8 8.8 1.0
NZ A:LYS400 3.8 12.0 1.0
OE1 A:GLU297 3.9 10.6 1.0
O A:HOH674 3.9 10.1 1.0
MG A:MG501 4.0 9.6 1.0
CG A:GLU297 4.0 10.0 1.0
C2 A:2PG503 4.1 15.0 1.0
NZ A:LYS349 4.1 14.2 1.0
NE2 A:GLN169 4.1 10.2 1.0
CD2 A:LEU347 4.1 9.9 1.0
OD2 A:ASP298 4.1 10.6 1.0
OD1 A:ASP324 4.2 9.6 1.0
CB A:ASP248 4.3 9.9 1.0
OE2 A:GLU170 4.6 11.7 1.0
C3 A:2PG503 4.9 15.6 1.0
CG A:ASP298 4.9 10.2 1.0
CB A:ALA250 4.9 9.5 1.0

Magnesium binding site 3 out of 6 in 7vrd

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Magnesium binding site 3 out of 6 in the Crystal Structure of ENOLASE1 From Candida Albicans Complexed with 2'- Phosphoglyceric Acid Sodium


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of ENOLASE1 From Candida Albicans Complexed with 2'- Phosphoglyceric Acid Sodium within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg501

b:14.8
occ:1.00
 O B:HOH785 2.0 18.6 1.0
OD2 B:ASP324 2.0 16.5 1.0
OE2 B:GLU297 2.1 16.6 1.0
OD2 B:ASP248 2.1 17.5 1.0
O B:HOH705 2.1 19.1 1.0
O B:HOH617 2.1 14.5 1.0
CG B:ASP248 3.0 17.3 1.0
CG B:ASP324 3.1 16.1 1.0
CD B:GLU297 3.2 15.8 1.0
OD1 B:ASP248 3.4 17.4 1.0
CB B:ASP324 3.6 15.7 1.0
OE1 B:GLU297 4.1 16.5 1.0
CG B:GLU297 4.1 15.5 1.0
O B:HOH648 4.1 30.1 1.0
O B:HOH741 4.1 24.1 1.0
NZ B:LYS400 4.1 18.6 1.0
O B:HOH621 4.2 26.4 1.0
OD1 B:ASP324 4.2 16.2 1.0
NE2 B:GLN169 4.2 21.8 1.0
OE2 B:GLU170 4.3 19.8 1.0
CB B:ASP248 4.3 17.0 1.0
OD2 B:ASP298 4.3 17.7 1.0
O B:HOH827 4.5 31.5 1.0
CD2 B:LEU347 4.5 20.0 1.0
CD B:GLU170 4.9 19.4 1.0
NZ B:LYS349 4.9 17.5 1.0

Magnesium binding site 4 out of 6 in 7vrd

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Magnesium binding site 4 out of 6 in the Crystal Structure of ENOLASE1 From Candida Albicans Complexed with 2'- Phosphoglyceric Acid Sodium


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of ENOLASE1 From Candida Albicans Complexed with 2'- Phosphoglyceric Acid Sodium within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg501

b:8.6
occ:1.00
 O C:SER41 2.0 9.7 1.0
O C:HOH695 2.0 8.8 1.0
O4P C:2PG503 2.1 10.3 1.0
O C:HOH636 2.1 9.2 1.0
OG C:SER41 2.2 10.1 1.0
O2 C:2PG503 2.2 12.7 1.0
C C:SER41 3.0 10.3 1.0
CB C:SER41 3.1 10.2 1.0
C1 C:2PG503 3.1 14.7 1.0
P C:2PG503 3.3 10.4 1.0
C2 C:2PG503 3.5 14.2 1.0
CA C:SER41 3.5 10.2 1.0
O1P C:2PG503 3.6 12.8 1.0
OD2 C:ASP324 3.9 9.9 1.0
NZ C:LYS349 3.9 16.5 1.0
O3P C:2PG503 3.9 10.4 1.0
MG C:MG502 4.0 9.7 1.0
OD1 C:ASP325 4.1 11.0 1.0
N C:SER41 4.1 10.5 1.0
NH2 C:ARG378 4.1 8.9 1.0
O1 C:2PG503 4.2 14.4 1.0
OD2 C:ASP325 4.2 11.4 1.0
O C:HOH643 4.2 8.9 1.0
N C:THR42 4.2 10.6 1.0
NE2 C:GLN169 4.2 9.9 1.0
OE1 C:GLN169 4.3 10.2 1.0
O2P C:2PG503 4.5 10.4 1.0
CG C:ASP325 4.5 10.7 1.0
CA C:THR42 4.7 11.5 1.0
CD C:GLN169 4.7 9.8 1.0
CG C:ASP324 4.9 9.5 1.0

Magnesium binding site 5 out of 6 in 7vrd

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Magnesium binding site 5 out of 6 in the Crystal Structure of ENOLASE1 From Candida Albicans Complexed with 2'- Phosphoglyceric Acid Sodium


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of ENOLASE1 From Candida Albicans Complexed with 2'- Phosphoglyceric Acid Sodium within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg502

b:9.7
occ:1.00
 OD2 C:ASP324 2.0 9.9 1.0
OE2 C:GLU297 2.0 10.7 1.0
O C:HOH643 2.1 8.9 1.0
OD2 C:ASP248 2.1 10.3 1.0
O1 C:2PG503 2.1 14.4 1.0
O2 C:2PG503 2.3 12.7 1.0
C1 C:2PG503 2.5 14.7 1.0
CG C:ASP248 3.0 9.8 1.0
CG C:ASP324 3.1 9.5 1.0
CD C:GLU297 3.2 10.2 1.0
OD1 C:ASP248 3.3 10.2 1.0
CB C:ASP324 3.6 9.2 1.0
O C:HOH636 3.8 9.2 1.0
NZ C:LYS400 3.9 11.8 1.0
OE1 C:GLU297 3.9 10.3 1.0
O C:HOH695 3.9 8.8 1.0
MG C:MG501 4.0 8.6 1.0
NZ C:LYS349 4.0 16.5 1.0
C2 C:2PG503 4.0 14.2 1.0
CG C:GLU297 4.1 10.0 1.0
OD2 C:ASP298 4.1 9.7 1.0
NE2 C:GLN169 4.1 9.9 1.0
CD2 C:LEU347 4.2 9.6 1.0
OD1 C:ASP324 4.2 9.6 1.0
CB C:ASP248 4.3 9.5 1.0
OE2 C:GLU170 4.6 10.9 1.0
C3 C:2PG503 4.9 15.4 1.0
CG C:ASP298 4.9 9.5 1.0
CB C:ALA250 4.9 9.0 1.0

Magnesium binding site 6 out of 6 in 7vrd

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Magnesium binding site 6 out of 6 in the Crystal Structure of ENOLASE1 From Candida Albicans Complexed with 2'- Phosphoglyceric Acid Sodium


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of ENOLASE1 From Candida Albicans Complexed with 2'- Phosphoglyceric Acid Sodium within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg501

b:13.7
occ:1.00
 O D:HOH620 2.0 14.5 1.0
OE2 D:GLU297 2.0 16.8 1.0
O D:HOH788 2.1 19.1 1.0
OD2 D:ASP324 2.1 18.4 1.0
OD2 D:ASP248 2.1 17.3 1.0
O D:HOH752 2.1 19.5 1.0
CG D:ASP248 3.0 16.9 1.0
CG D:ASP324 3.1 18.2 1.0
CD D:GLU297 3.2 16.1 1.0
OD1 D:ASP248 3.4 17.0 1.0
CB D:ASP324 3.6 17.6 1.0
O D:HOH618 4.0 29.8 1.0
CG D:GLU297 4.0 15.7 1.0
OE1 D:GLU297 4.0 16.6 1.0
NZ D:LYS400 4.1 19.9 1.0
O D:HOH770 4.2 26.4 1.0
OE2 D:GLU170 4.2 19.9 1.0
O D:HOH637 4.2 27.0 1.0
OD2 D:ASP298 4.2 15.7 1.0
OD1 D:ASP324 4.2 18.6 1.0
NE2 D:GLN169 4.3 19.1 1.0
CB D:ASP248 4.3 16.5 1.0
O D:HOH827 4.5 29.7 1.0
CD2 D:LEU347 4.6 20.1 1.0
CD D:GLU170 4.8 19.2 1.0
O D:HOH768 4.9 29.0 1.0

Reference:

M.Zhang, X.Zhang. Crystal Structure of ENOLASE1 From Candida Albicans Complexed with 2'-Phosphoglyceric Acid Sodium at 1.7 Angstroms To Be Published.
Page generated: Thu Oct 3 10:38:29 2024

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