Calcium 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:

Magnesium (Mg) 4 atoms

Calcium Binding Sites:

The binding sites of Calcium 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 Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure of Suca with Glycolaldehyde-1-13C From Vibrio Vulnificus, PDB code: 6kma:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 6kma

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


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca 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:Ca1002

b:41.1
occ:1.00
OE1 A:GLU665 2.4 30.7 1.0
O B:HOH1164 2.4 38.8 1.0
O A:HOH1164 2.4 32.1 1.0
O B:HOH1138 2.4 27.3 1.0
OE1 B:GLU665 2.4 33.5 1.0
O B:HOH1202 2.4 32.2 1.0
CD A:GLU665 3.3 30.9 1.0
CD B:GLU665 3.4 32.1 1.0
OE2 A:GLU665 3.7 34.1 1.0
OE2 B:GLU665 3.8 33.5 1.0
O A:HOH1285 4.3 33.5 1.0
O B:HOH1285 4.3 23.5 1.0
O A:GLY695 4.4 21.6 1.0
O B:GLY695 4.4 18.3 1.0
O A:HOH1325 4.5 25.6 1.0
CG A:GLU665 4.5 28.8 1.0
CB A:GLU665 4.5 25.5 1.0
CG B:GLU665 4.6 29.2 1.0
CB B:GLU665 4.6 28.4 1.0
OE2 B:GLU371 4.7 25.5 1.0
OE2 A:GLU371 4.7 21.5 1.0
O B:HOH1309 5.0 33.4 1.0
O A:HOH1261 5.0 18.2 1.0

Calcium binding site 2 out of 2 in 6kma

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


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca 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
C:Ca1002

b:45.0
occ:1.00
O D:HOH1124 2.4 38.9 1.0
O C:HOH1131 2.4 36.0 1.0
O C:HOH1180 2.4 26.7 1.0
OE1 D:GLU665 2.4 35.8 1.0
O C:HOH1191 2.4 25.9 1.0
OE1 C:GLU665 2.4 29.9 1.0
CD C:GLU665 3.4 29.8 1.0
CD D:GLU665 3.4 35.5 1.0
OE2 C:GLU665 3.8 31.9 1.0
O C:HOH1334 3.8 32.4 1.0
O D:HOH1102 3.9 36.1 1.0
OE2 D:GLU665 3.9 38.1 1.0
O C:HOH1347 4.2 30.4 1.0
O D:GLY695 4.3 23.3 1.0
O D:HOH1237 4.4 26.8 1.0
CB D:GLU665 4.5 32.7 1.0
OE2 D:GLU371 4.5 32.1 1.0
CG D:GLU665 4.5 33.9 1.0
O C:GLY695 4.6 24.3 1.0
CG C:GLU665 4.6 28.4 1.0
CB C:GLU665 4.7 27.1 1.0
OE2 C:GLU371 4.8 23.3 1.0
O D:HOH1223 4.9 18.6 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: Sat Dec 12 06:18:27 2020

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