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Calcium in PDB 9evj: Crystal Structure of Human Collagen Hydroxylysine Galactosyltransferase GLT25D1/COLGALT1: Complex with MN2+ and Udp-Gal

Enzymatic activity of Crystal Structure of Human Collagen Hydroxylysine Galactosyltransferase GLT25D1/COLGALT1: Complex with MN2+ and Udp-Gal

All present enzymatic activity of Crystal Structure of Human Collagen Hydroxylysine Galactosyltransferase GLT25D1/COLGALT1: Complex with MN2+ and Udp-Gal:
2.4.1.50;

Protein crystallography data

The structure of Crystal Structure of Human Collagen Hydroxylysine Galactosyltransferase GLT25D1/COLGALT1: Complex with MN2+ and Udp-Gal, PDB code: 9evj was solved by M.De Marco, L.Scietti, S.R.Rai, D.Mattoteia, A.Pinnola, F.Forneris, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.38 / 2.70
Space group I 2 3
Cell size a, b, c (Å), α, β, γ (°) 220.855, 220.855, 220.855, 90, 90, 90
R / Rfree (%) 18.6 / 22.3

Other elements in 9evj:

The structure of Crystal Structure of Human Collagen Hydroxylysine Galactosyltransferase GLT25D1/COLGALT1: Complex with MN2+ and Udp-Gal also contains other interesting chemical elements:

Sodium (Na) 1 atom
Chlorine (Cl) 6 atoms
Manganese (Mn) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Human Collagen Hydroxylysine Galactosyltransferase GLT25D1/COLGALT1: Complex with MN2+ and Udp-Gal (pdb code 9evj). 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 Human Collagen Hydroxylysine Galactosyltransferase GLT25D1/COLGALT1: Complex with MN2+ and Udp-Gal, PDB code: 9evj:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 9evj

Go back to Calcium Binding Sites List in 9evj
Calcium binding site 1 out of 2 in the Crystal Structure of Human Collagen Hydroxylysine Galactosyltransferase GLT25D1/COLGALT1: Complex with MN2+ and Udp-Gal


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 Human Collagen Hydroxylysine Galactosyltransferase GLT25D1/COLGALT1: Complex with MN2+ and Udp-Gal within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca709

b:49.7
occ:1.00
 O1B A:GDU701 2.2 48.2 1.0
OD2 A:ASP168 2.2 63.0 1.0
O1A A:GDU701 2.5 56.0 1.0
O A:HOH848 2.6 67.0 1.0
OD1 A:ASP168 2.7 52.9 1.0
O A:HOH837 2.7 71.9 1.0
CG A:ASP168 2.8 51.2 1.0
O A:HOH817 2.9 64.4 1.0
O3A A:GDU701 3.2 56.5 1.0
PB A:GDU701 3.2 46.8 1.0
PA A:GDU701 3.4 58.9 1.0
O3B A:GDU701 4.1 67.2 1.0
O2A A:GDU701 4.3 62.8 1.0
CB A:ASP168 4.3 40.9 1.0
O2B A:GDU701 4.4 56.7 1.0
CG A:PRO292 4.5 44.6 1.0
OE2 A:GLU304 4.6 79.2 1.0
OD2 A:ASP166 4.6 69.2 1.0
O5D A:GDU701 4.6 78.8 1.0
ND2 A:ASN169 4.7 59.1 1.0
C5D A:GDU701 4.7 57.7 1.0
C1' A:GDU701 4.7 40.4 1.0
O A:PRO292 4.8 52.5 1.0
CD A:PRO292 4.9 54.9 1.0
CB A:ASP166 5.0 49.6 1.0

Calcium binding site 2 out of 2 in 9evj

Go back to Calcium Binding Sites List in 9evj
Calcium binding site 2 out of 2 in the Crystal Structure of Human Collagen Hydroxylysine Galactosyltransferase GLT25D1/COLGALT1: Complex with MN2+ and Udp-Gal


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 Human Collagen Hydroxylysine Galactosyltransferase GLT25D1/COLGALT1: Complex with MN2+ and Udp-Gal within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca706

b:62.4
occ:1.00
 OD2 B:ASP168 2.2 52.6 1.0
O2B B:GDU701 2.3 63.5 1.0
O1A B:GDU701 2.4 71.5 1.0
O B:HOH842 2.4 62.8 1.0
O B:HOH806 2.8 65.9 1.0
PB B:GDU701 3.1 58.5 1.0
CG B:ASP168 3.1 63.4 1.0
PA B:GDU701 3.1 48.5 1.0
O3B B:GDU701 3.2 54.1 1.0
O5D B:GDU701 3.2 65.0 1.0
OD1 B:ASP168 3.3 74.9 1.0
O3A B:GDU701 3.5 46.2 1.0
C1' B:GDU701 4.3 63.0 1.0
OD2 B:ASP166 4.3 68.5 1.0
O1B B:GDU701 4.5 71.0 1.0
CB B:ASP168 4.5 38.8 1.0
O2A B:GDU701 4.6 50.0 1.0
C5D B:GDU701 4.6 45.5 1.0
O5' B:GDU701 4.8 47.0 1.0
CG B:PRO292 4.9 46.4 1.0
O B:HOH815 4.9 60.9 1.0
ND2 B:ASN169 5.0 58.0 1.0

Reference:

M.De Marco, L.Scietti, S.R.Rai, D.Mattoteia, M.Fumagalli, A.Pinnola, F.Forneris. Crystal Structure of Human Collagen Hydroxylysine Galactosyltransferase GLT25D1/COLGALT1: Complex with MN2+ and Udp-Gal To Be Published.
Page generated: Thu Jul 10 09:35:13 2025

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