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Calcium in PDB 2yi1: Crystal Structure of N-Acetylmannosamine Kinase in Complex with N-Acetyl Mannosamine 6-Phosphate and Adp.

Enzymatic activity of Crystal Structure of N-Acetylmannosamine Kinase in Complex with N-Acetyl Mannosamine 6-Phosphate and Adp.

All present enzymatic activity of Crystal Structure of N-Acetylmannosamine Kinase in Complex with N-Acetyl Mannosamine 6-Phosphate and Adp.:
2.7.1.60;

Protein crystallography data

The structure of Crystal Structure of N-Acetylmannosamine Kinase in Complex with N-Acetyl Mannosamine 6-Phosphate and Adp., PDB code: 2yi1 was solved by J.Martinez, L.D.Nguyen, E.Tauberger, S.Hinderlich, W.Reutter, H.Fan, W.Saenger, S.Moniot, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.40 / 2.15
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 90.700, 90.700, 101.490, 90.00, 90.00, 90.00
R / Rfree (%) 16.667 / 19.101

Other elements in 2yi1:

The structure of Crystal Structure of N-Acetylmannosamine Kinase in Complex with N-Acetyl Mannosamine 6-Phosphate and Adp. also contains other interesting chemical elements:

Magnesium (Mg) 1 atom
Zinc (Zn) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of N-Acetylmannosamine Kinase in Complex with N-Acetyl Mannosamine 6-Phosphate and Adp. (pdb code 2yi1). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Crystal Structure of N-Acetylmannosamine Kinase in Complex with N-Acetyl Mannosamine 6-Phosphate and Adp., PDB code: 2yi1:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in 2yi1

Go back to Calcium Binding Sites List in 2yi1
Calcium binding site 1 out of 3 in the Crystal Structure of N-Acetylmannosamine Kinase in Complex with N-Acetyl Mannosamine 6-Phosphate and Adp.


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 N-Acetylmannosamine Kinase in Complex with N-Acetyl Mannosamine 6-Phosphate and Adp. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1718

b:31.9
occ:1.00
 NE2 A:GLN493 3.1 24.0 1.0
O A:HOH2057 3.2 18.8 1.0
CD A:GLN493 4.1 27.6 1.0
CG A:GLN493 4.1 24.5 1.0
CD A:LYS490 4.3 33.8 1.0
CB A:LYS490 4.4 26.4 1.0
CG A:LYS490 4.9 29.8 1.0
O A:LYS490 5.0 24.4 1.0

Calcium binding site 2 out of 3 in 2yi1

Go back to Calcium Binding Sites List in 2yi1
Calcium binding site 2 out of 3 in the Crystal Structure of N-Acetylmannosamine Kinase in Complex with N-Acetyl Mannosamine 6-Phosphate and Adp.


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 N-Acetylmannosamine Kinase in Complex with N-Acetyl Mannosamine 6-Phosphate and Adp. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1719

b:22.8
occ:0.65
 CA A:CA1719 0.0 22.8 0.7
CA A:CA1719 1.8 26.2 0.3
O A:GLY548 2.5 17.9 1.0
OD1 A:ASN516 2.5 20.8 1.0
O A:HOH2066 2.5 15.2 1.0
O A:ALA565 2.6 20.4 1.0
CG A:ASN516 3.3 19.2 1.0
C A:ALA565 3.3 20.6 1.0
OD1 A:ASN519 3.5 24.1 1.0
C A:GLY548 3.5 19.8 1.0
CB A:ALA565 3.8 21.2 1.0
O A:HOH2046 3.9 30.0 1.0
O A:ALA564 3.9 21.2 1.0
N A:GLY548 3.9 20.9 1.0
ND2 A:ASN516 4.0 19.8 1.0
N A:ASN519 4.1 20.1 1.0
N A:GLU566 4.1 20.1 1.0
CG A:ASN519 4.1 24.2 1.0
CA A:ALA565 4.2 21.2 1.0
CA A:GLY548 4.2 20.4 1.0
CB A:ASN516 4.2 19.9 1.0
CA A:GLY518 4.3 19.5 1.0
CA A:GLU566 4.4 18.6 1.0
C A:GLY518 4.4 19.8 1.0
OE2 A:GLU566 4.5 23.4 1.0
N A:GLY549 4.6 18.8 1.0
ND2 A:ASN519 4.6 20.0 1.0
N A:GLY518 4.6 19.6 1.0
CD A:GLU566 4.7 20.5 1.0
CG A:GLU566 4.8 17.0 1.0
CA A:GLY549 4.8 19.7 1.0
O4 A:BM31001 4.8 18.3 0.6
O A:HOH2068 4.9 24.2 1.0
C A:ALA564 4.9 22.0 1.0
CA A:ASN519 4.9 19.8 1.0
O4 A:BMX1000 5.0 21.8 0.4

Calcium binding site 3 out of 3 in 2yi1

Go back to Calcium Binding Sites List in 2yi1
Calcium binding site 3 out of 3 in the Crystal Structure of N-Acetylmannosamine Kinase in Complex with N-Acetyl Mannosamine 6-Phosphate and Adp.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of N-Acetylmannosamine Kinase in Complex with N-Acetyl Mannosamine 6-Phosphate and Adp. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1719

b:26.2
occ:0.35
 CA A:CA1719 0.0 26.2 0.3
CA A:CA1719 1.8 22.8 0.7
O A:HOH2046 2.5 30.0 1.0
O A:ALA564 2.8 21.2 1.0
OD1 A:ASN516 3.2 20.8 1.0
O A:ALA565 3.4 20.4 1.0
O A:HOH2068 3.4 24.2 1.0
CG A:ASN516 3.4 19.2 1.0
C A:ALA565 3.5 20.6 1.0
OD1 A:ASN519 3.6 24.1 1.0
O A:HOH2066 3.7 15.2 1.0
CB A:ASN516 3.9 19.9 1.0
C A:ALA564 3.9 22.0 1.0
ND2 A:ASN519 4.0 20.0 1.0
N A:GLU566 4.0 20.1 1.0
CG A:ASN519 4.0 24.2 1.0
OE2 A:GLU566 4.0 23.4 1.0
ND2 A:ASN516 4.0 19.8 1.0
CG A:GLU566 4.1 17.0 1.0
CB A:ALA565 4.1 21.2 1.0
O A:GLY548 4.1 17.9 1.0
CA A:ALA565 4.2 21.2 1.0
O A:HOH2047 4.2 16.0 1.0
CD A:GLU566 4.3 20.5 1.0
CA A:GLU566 4.4 18.6 1.0
N A:ALA565 4.5 21.7 1.0
CB A:GLU566 4.8 19.1 1.0

Reference:

J.Martinez, L.D.Nguyen, E.Tauberger, S.Hinderlich, W.Reutter, H.Fan, W.Saenger, S.Moniot. Crystal Structures of N-Acetylmannosamine Kinase Provide Insights Into Enzyme Specificity and Inhibition J.Biol.Chem. V. 287 13656 2012.
ISSN: ISSN 0021-9258
PubMed: 22343627
DOI: 10.1074/JBC.M111.318170
Page generated: Sat Dec 12 04:00:35 2020

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