Atomistry » Magnesium » PDB 6ki8-6kql » 6kma
Atomistry »
  Magnesium »
    PDB 6ki8-6kql »
      6kma »

Magnesium in PDB 6kma: Crystal Structure of Suca with Glycolaldehyde-1-13C From Vibrio Vulnificus

Enzymatic activity of Crystal Structure of Suca with Glycolaldehyde-1-13C From Vibrio Vulnificus

All present enzymatic activity of Crystal Structure of Suca with Glycolaldehyde-1-13C From Vibrio Vulnificus:
1.2.4.2;

Protein crystallography data

The structure of Crystal Structure of Suca with Glycolaldehyde-1-13C From Vibrio Vulnificus, PDB code: 6kma was solved by P.W.Seo, J.S.Kim, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.65 / 2.28
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 76.820, 84.559, 145.218, 79.51, 88.47, 89.92
R / Rfree (%) 20 / 23

Other elements in 6kma:

The structure of Crystal Structure of Suca with Glycolaldehyde-1-13C From Vibrio Vulnificus also contains other interesting chemical elements:

Calcium (Ca) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Suca with Glycolaldehyde-1-13C From Vibrio Vulnificus (pdb code 6kma). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of Suca with Glycolaldehyde-1-13C From Vibrio Vulnificus, PDB code: 6kma:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 6kma

Go back to Magnesium Binding Sites List in 6kma
Magnesium binding site 1 out of 4 in the Crystal Structure of Suca with Glycolaldehyde-1-13C From Vibrio Vulnificus


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 Suca with Glycolaldehyde-1-13C From Vibrio Vulnificus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1003

b:19.9
occ:1.00
 OD1 A:ASP360 2.0 28.1 1.0
O2A A:TPP1004 2.1 23.9 1.0
OD1 A:ASN393 2.1 26.6 1.0
O2B A:TPP1004 2.2 24.7 1.0
O A:VAL395 2.3 29.4 1.0
O A:HOH1113 2.6 20.1 1.0
CG A:ASP360 3.0 26.6 1.0
CG A:ASN393 3.1 25.7 1.0
PB A:TPP1004 3.2 24.1 1.0
PA A:TPP1004 3.3 22.8 1.0
OD2 A:ASP360 3.3 29.6 1.0
ND2 A:ASN393 3.4 25.8 1.0
C A:VAL395 3.5 27.5 1.0
O3A A:TPP1004 3.6 22.9 1.0
O3B A:TPP1004 3.7 26.5 1.0
N A:ASP360 4.0 22.7 1.0
N A:VAL395 4.2 25.5 1.0
O7 A:TPP1004 4.3 22.6 1.0
O A:VAL391 4.3 23.0 1.0
CB A:ASP360 4.3 24.6 1.0
O1A A:TPP1004 4.3 22.2 1.0
N A:ASN393 4.4 26.4 1.0
N A:GLY396 4.4 26.4 1.0
CA A:GLY396 4.4 26.9 1.0
CB A:ASN393 4.4 25.4 1.0
N A:SER361 4.5 22.6 1.0
CA A:VAL395 4.5 26.6 1.0
O1B A:TPP1004 4.5 22.0 1.0
O A:HOH1173 4.6 23.0 1.0
CA A:ASP360 4.7 24.1 1.0
N A:GLN394 4.7 25.3 1.0
CA A:ASN393 4.8 26.3 1.0
CG1 A:VAL395 4.8 29.7 1.0
C A:ASN393 4.8 24.8 1.0
C A:GLY359 4.9 23.8 1.0
CA A:GLY359 4.9 23.3 1.0

Magnesium binding site 2 out of 4 in 6kma

Go back to Magnesium Binding Sites List in 6kma
Magnesium binding site 2 out of 4 in the Crystal Structure of Suca with Glycolaldehyde-1-13C From Vibrio Vulnificus


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 Suca with Glycolaldehyde-1-13C From Vibrio Vulnificus within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1003

b:21.6
occ:1.00
 OD1 B:ASP360 2.0 27.9 1.0
O2A B:TPP1004 2.1 24.6 1.0
OD1 B:ASN393 2.1 28.8 1.0
O2B B:TPP1004 2.2 22.7 1.0
O B:VAL395 2.2 30.0 1.0
O B:HOH1117 2.2 20.2 1.0
CG B:ASP360 3.0 29.3 1.0
CG B:ASN393 3.1 28.3 1.0
OD2 B:ASP360 3.3 29.8 1.0
PB B:TPP1004 3.3 22.6 1.0
PA B:TPP1004 3.3 23.4 1.0
C B:VAL395 3.4 28.2 1.0
ND2 B:ASN393 3.5 26.7 1.0
O3A B:TPP1004 3.7 25.9 1.0
O3B B:TPP1004 3.8 23.1 1.0
N B:VAL395 4.1 26.5 1.0
N B:ASP360 4.1 25.7 1.0
N B:GLY396 4.2 23.5 1.0
O7 B:TPP1004 4.3 22.8 1.0
CA B:GLY396 4.3 22.0 1.0
CB B:ASP360 4.3 26.0 1.0
CA B:VAL395 4.4 28.8 1.0
O B:VAL391 4.4 27.1 1.0
N B:ASN393 4.4 29.7 1.0
O1A B:TPP1004 4.4 26.9 1.0
O B:HOH1193 4.5 19.6 1.0
CB B:ASN393 4.5 28.5 1.0
N B:SER361 4.5 21.3 1.0
O1B B:TPP1004 4.6 23.8 1.0
CG1 B:VAL395 4.6 33.0 1.0
N B:GLN394 4.7 30.6 1.0
CA B:ASP360 4.7 25.8 1.0
CA B:ASN393 4.8 30.1 1.0
C B:ASN393 4.8 31.2 1.0

Magnesium binding site 3 out of 4 in 6kma

Go back to Magnesium Binding Sites List in 6kma
Magnesium binding site 3 out of 4 in the Crystal Structure of Suca with Glycolaldehyde-1-13C From Vibrio Vulnificus


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 Suca with Glycolaldehyde-1-13C From Vibrio Vulnificus within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1003

b:22.9
occ:1.00
 OD1 C:ASN393 2.0 26.1 1.0
OD1 C:ASP360 2.1 41.3 1.0
O1A C:TPP1004 2.1 30.9 1.0
O1B C:TPP1004 2.2 24.5 1.0
O C:VAL395 2.2 27.3 1.0
O C:HOH1165 2.4 20.1 1.0
CG C:ASP360 3.1 38.6 1.0
CG C:ASN393 3.1 22.7 1.0
PA C:TPP1004 3.4 18.2 1.0
OD2 C:ASP360 3.4 40.6 1.0
C C:VAL395 3.4 27.4 1.0
PB C:TPP1004 3.4 24.4 1.0
ND2 C:ASN393 3.5 20.7 1.0
O3A C:TPP1004 3.6 26.2 1.0
N C:VAL395 4.0 27.1 1.0
N C:ASP360 4.1 25.4 1.0
O3B C:TPP1004 4.1 23.7 1.0
N C:GLY396 4.2 27.1 1.0
N C:ASN393 4.3 25.3 1.0
O7 C:TPP1004 4.3 23.9 1.0
CA C:VAL395 4.3 28.0 1.0
O C:VAL391 4.3 25.5 1.0
CA C:GLY396 4.3 24.9 1.0
CB C:ASP360 4.4 31.6 1.0
CB C:ASN393 4.4 24.4 1.0
O2A C:TPP1004 4.4 22.9 1.0
N C:SER361 4.5 23.6 1.0
N C:GLN394 4.5 27.3 1.0
O2B C:TPP1004 4.5 24.1 1.0
C C:ASN393 4.6 26.8 1.0
CA C:ASN393 4.6 25.6 1.0
O C:HOH1171 4.7 18.9 1.0
CA C:ASP360 4.8 27.2 1.0
CG1 C:VAL395 4.8 29.7 1.0
C C:GLY359 5.0 24.2 1.0
CA C:GLY359 5.0 23.6 1.0

Magnesium binding site 4 out of 4 in 6kma

Go back to Magnesium Binding Sites List in 6kma
Magnesium binding site 4 out of 4 in the Crystal Structure of Suca with Glycolaldehyde-1-13C From Vibrio Vulnificus


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 Suca with Glycolaldehyde-1-13C From Vibrio Vulnificus within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg1003

b:20.2
occ:1.00
 OD1 D:ASP360 2.0 29.4 1.0
O1A D:TPP1004 2.1 26.6 1.0
O D:VAL395 2.1 26.3 1.0
OD1 D:ASN393 2.1 25.9 1.0
O1B D:TPP1004 2.2 19.1 1.0
O D:HOH1142 2.4 18.8 1.0
CG D:ASP360 2.9 27.9 1.0
CG D:ASN393 3.2 25.3 1.0
OD2 D:ASP360 3.2 29.5 1.0
C D:VAL395 3.3 26.4 1.0
PA D:TPP1004 3.4 22.2 1.0
PB D:TPP1004 3.4 23.4 1.0
ND2 D:ASN393 3.6 27.2 1.0
O3A D:TPP1004 3.7 22.8 1.0
N D:VAL395 4.0 24.0 1.0
N D:ASP360 4.1 26.2 1.0
O3B D:TPP1004 4.1 22.1 1.0
N D:GLY396 4.1 25.6 1.0
CA D:GLY396 4.2 24.9 1.0
CA D:VAL395 4.3 23.6 1.0
CB D:ASP360 4.3 26.3 1.0
O7 D:TPP1004 4.3 22.9 1.0
N D:ASN393 4.4 27.1 1.0
O D:VAL391 4.4 27.5 1.0
N D:SER361 4.4 23.8 1.0
O2A D:TPP1004 4.4 27.0 1.0
O D:HOH1169 4.4 19.5 1.0
CB D:ASN393 4.5 25.3 1.0
O2B D:TPP1004 4.6 21.9 1.0
N D:GLN394 4.6 25.3 1.0
CA D:ASP360 4.7 25.6 1.0
CG1 D:VAL395 4.7 26.1 1.0
C D:ASN393 4.8 26.6 1.0
CA D:ASN393 4.8 26.2 1.0
OG D:SER361 5.0 28.0 1.0
C D:GLY359 5.0 25.6 1.0

Reference:

P.W.Seo, J.S.Kim. Crystal Structure of Suca with Glycolaldehyde-1-13C From Vibrio Vulnificus at 2.28 Angstroms Resolution. To Be Published.
Page generated: Tue Oct 1 07:16:58 2024

Last articles

Mg in 4JI0
Mg in 4JI2
Mg in 4JI3
Mg in 4JHD
Mg in 4JH6
Mg in 4JH8
Mg in 4JH7
Mg in 4JH3
Mg in 4JH5
Mg in 4JF2
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy