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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

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