Atomistry » Calcium » PDB 1h80-1hny » 1hm9
Atomistry »
  Calcium »
    PDB 1h80-1hny »
      1hm9 »

Calcium in PDB 1hm9: Crystal Structure of S.Pneumoniae N-Acetylglucosamine-1-Phosphate Uridyltransferase, Glmu, Bound to Acetyl Coenzyme A and Udp-N- Acetylglucosamine

Enzymatic activity of Crystal Structure of S.Pneumoniae N-Acetylglucosamine-1-Phosphate Uridyltransferase, Glmu, Bound to Acetyl Coenzyme A and Udp-N- Acetylglucosamine

All present enzymatic activity of Crystal Structure of S.Pneumoniae N-Acetylglucosamine-1-Phosphate Uridyltransferase, Glmu, Bound to Acetyl Coenzyme A and Udp-N- Acetylglucosamine:
2.7.7.23;

Protein crystallography data

The structure of Crystal Structure of S.Pneumoniae N-Acetylglucosamine-1-Phosphate Uridyltransferase, Glmu, Bound to Acetyl Coenzyme A and Udp-N- Acetylglucosamine, PDB code: 1hm9 was solved by G.Sulzenbacher, L.Gal, C.Peneff, F.Fassy, Y.Bourne, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.14 / 1.75
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 89.509, 89.509, 278.753, 90.00, 90.00, 120.00
R / Rfree (%) 18.3 / 21.9

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of S.Pneumoniae N-Acetylglucosamine-1-Phosphate Uridyltransferase, Glmu, Bound to Acetyl Coenzyme A and Udp-N- Acetylglucosamine (pdb code 1hm9). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Crystal Structure of S.Pneumoniae N-Acetylglucosamine-1-Phosphate Uridyltransferase, Glmu, Bound to Acetyl Coenzyme A and Udp-N- Acetylglucosamine, PDB code: 1hm9:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 1hm9

Go back to Calcium Binding Sites List in 1hm9
Calcium binding site 1 out of 8 in the Crystal Structure of S.Pneumoniae N-Acetylglucosamine-1-Phosphate Uridyltransferase, Glmu, Bound to Acetyl Coenzyme A and Udp-N- Acetylglucosamine


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 S.Pneumoniae N-Acetylglucosamine-1-Phosphate Uridyltransferase, Glmu, Bound to Acetyl Coenzyme A and Udp-N- Acetylglucosamine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1901

b:20.0
occ:1.00
 OD1 A:ASN227 2.2 18.5 1.0
O A:HOH1068 2.3 14.6 1.0
O2A A:UD11500 2.3 19.8 1.0
O A:HOH1061 2.3 21.8 1.0
OD2 A:ASP102 2.4 18.1 1.0
O2B A:UD11500 2.4 20.3 1.0
CG A:ASN227 3.2 17.8 1.0
CG A:ASP102 3.3 18.5 1.0
PA A:UD11500 3.4 21.0 1.0
PB A:UD11500 3.5 20.2 1.0
O3A A:UD11500 3.5 19.6 1.0
OD1 A:ASP102 3.6 17.1 1.0
ND2 A:ASN227 3.6 20.1 1.0
NZ A:LYS22 3.8 18.3 1.0
O6' A:UD11500 3.9 23.7 1.0
O5' A:UD11500 4.3 18.8 1.0
O5B A:UD11500 4.3 20.1 1.0
C5B A:UD11500 4.3 17.5 1.0
O A:VAL226 4.4 12.9 1.0
O1B A:UD11500 4.5 22.0 1.0
O A:HOH1172 4.5 29.0 1.0
O1' A:UD11500 4.6 20.5 1.0
CB A:ASN227 4.6 17.8 1.0
O1A A:UD11500 4.6 23.4 1.0
CB A:ASP102 4.7 17.3 1.0
C A:VAL226 4.7 13.2 1.0
C1' A:UD11500 4.8 20.0 1.0
NH2 A:ARG15 4.8 12.3 0.3
N A:VAL226 4.9 17.2 1.0
C5' A:UD11500 4.9 21.6 1.0
CA A:ASN227 4.9 14.0 1.0
C A:GLY225 4.9 16.0 1.0
N A:ASN227 4.9 12.8 1.0
C3B A:UD11500 4.9 20.9 1.0
CA A:GLY225 5.0 17.2 1.0

Calcium binding site 2 out of 8 in 1hm9

Go back to Calcium Binding Sites List in 1hm9
Calcium binding site 2 out of 8 in the Crystal Structure of S.Pneumoniae N-Acetylglucosamine-1-Phosphate Uridyltransferase, Glmu, Bound to Acetyl Coenzyme A and Udp-N- Acetylglucosamine


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 S.Pneumoniae N-Acetylglucosamine-1-Phosphate Uridyltransferase, Glmu, Bound to Acetyl Coenzyme A and Udp-N- Acetylglucosamine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1902

b:27.9
occ:1.00
 O A:HOH1251 1.8 27.7 1.0
O A:HOH1250 2.3 27.7 1.0
O1A A:UD11500 2.3 23.4 1.0
O A:HOH1342 2.4 53.6 1.0
NH1 A:ARG15 2.7 30.0 0.7
CZ A:ARG15 3.7 22.7 0.7
PA A:UD11500 3.8 21.0 1.0
NH2 A:ARG15 3.9 20.0 0.7
O A:HOH1311 4.1 41.8 1.0
NH2 A:ARG15 4.3 12.3 0.3
O A:HOH1120 4.4 23.1 1.0
OE1 A:GLU195 4.5 32.2 1.0
O A:HOH1249 4.5 10.7 1.0
O5B A:UD11500 4.5 20.1 1.0
O3A A:UD11500 4.6 19.6 1.0
OE2 A:GLU195 4.6 34.9 1.0
O1B A:UD11500 4.6 22.0 1.0
O2A A:UD11500 4.6 19.8 1.0
NE2 A:GLN193 4.6 43.2 1.0
C5 A:UD11500 4.7 25.5 1.0
C6 A:UD11500 4.8 24.5 1.0
NE A:ARG15 4.9 20.7 0.7
CD A:GLU195 5.0 36.4 1.0

Calcium binding site 3 out of 8 in 1hm9

Go back to Calcium Binding Sites List in 1hm9
Calcium binding site 3 out of 8 in the Crystal Structure of S.Pneumoniae N-Acetylglucosamine-1-Phosphate Uridyltransferase, Glmu, Bound to Acetyl Coenzyme A and Udp-N- Acetylglucosamine


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 S.Pneumoniae N-Acetylglucosamine-1-Phosphate Uridyltransferase, Glmu, Bound to Acetyl Coenzyme A and Udp-N- Acetylglucosamine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1903

b:37.5
occ:1.00
 OD1 A:ASP416 2.5 16.8 1.0
OD2 A:ASP416 2.5 26.8 1.0
O A:HOH1223 2.8 38.0 1.0
CG A:ASP416 2.8 23.1 1.0
OD2 A:ASP398 3.0 30.8 1.0
CG A:ASP398 3.7 23.5 1.0
O A:HOH1268 4.0 29.1 1.0
N A:ASP398 4.0 16.5 1.0
O A:HOH1087 4.3 28.0 1.0
OD1 A:ASP398 4.3 20.1 1.0
CB A:ASP416 4.4 16.2 1.0
CB A:ASP398 4.4 17.9 1.0
CA A:GLY397 4.6 16.4 1.0
O A:HOH1050 4.6 21.8 1.0
C A:GLY397 4.8 17.8 1.0
CA A:ASP398 4.9 15.6 1.0

Calcium binding site 4 out of 8 in 1hm9

Go back to Calcium Binding Sites List in 1hm9
Calcium binding site 4 out of 8 in the Crystal Structure of S.Pneumoniae N-Acetylglucosamine-1-Phosphate Uridyltransferase, Glmu, Bound to Acetyl Coenzyme A and Udp-N- Acetylglucosamine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of S.Pneumoniae N-Acetylglucosamine-1-Phosphate Uridyltransferase, Glmu, Bound to Acetyl Coenzyme A and Udp-N- Acetylglucosamine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1904

b:25.6
occ:0.33
 O A:HOH1254 2.1 14.4 1.0
OD1 A:ASN405 2.3 27.6 1.0
CG A:ASN405 3.4 25.3 1.0
ND2 A:ASN405 3.9 24.6 1.0
O A:GLY380 4.2 13.1 1.0
O A:HOH1024 4.5 17.7 1.0
CB A:ASN405 4.6 17.8 1.0
CA A:ASN405 4.8 14.5 1.0
CA A:GLY380 4.9 13.9 1.0
C A:GLY380 5.0 12.0 1.0

Calcium binding site 5 out of 8 in 1hm9

Go back to Calcium Binding Sites List in 1hm9
Calcium binding site 5 out of 8 in the Crystal Structure of S.Pneumoniae N-Acetylglucosamine-1-Phosphate Uridyltransferase, Glmu, Bound to Acetyl Coenzyme A and Udp-N- Acetylglucosamine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of S.Pneumoniae N-Acetylglucosamine-1-Phosphate Uridyltransferase, Glmu, Bound to Acetyl Coenzyme A and Udp-N- Acetylglucosamine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca2901

b:20.7
occ:1.00
 OD1 B:ASN227 2.2 17.8 1.0
O2A B:UD12500 2.3 18.2 1.0
O B:HOH2250 2.3 17.0 1.0
O B:HOH2251 2.4 18.1 1.0
O2B B:UD12500 2.4 18.9 1.0
OD2 B:ASP102 2.4 17.2 1.0
CG B:ASN227 3.2 17.7 1.0
CG B:ASP102 3.3 20.1 1.0
PA B:UD12500 3.4 21.5 1.0
PB B:UD12500 3.4 22.1 1.0
O3A B:UD12500 3.5 19.8 1.0
ND2 B:ASN227 3.6 19.1 1.0
OD1 B:ASP102 3.6 18.5 1.0
O6' B:UD12500 3.8 22.6 1.0
NZ B:LYS22 3.9 18.3 1.0
O5' B:UD12500 4.2 18.2 1.0
C5B B:UD12500 4.2 18.6 1.0
O5B B:UD12500 4.3 20.6 1.0
O B:HOH2129 4.3 34.4 1.0
O B:VAL226 4.4 12.5 1.0
O1B B:UD12500 4.4 23.9 1.0
O1' B:UD12500 4.5 22.8 1.0
CB B:ASN227 4.6 15.5 1.0
O1A B:UD12500 4.6 19.8 1.0
CB B:ASP102 4.7 18.8 1.0
C B:VAL226 4.7 13.6 1.0
C1' B:UD12500 4.7 21.6 1.0
C5' B:UD12500 4.8 21.0 1.0
N B:VAL226 4.8 16.8 1.0
CA B:ASN227 4.9 13.9 1.0
N B:ASN227 4.9 12.4 1.0
C6' B:UD12500 4.9 21.7 1.0
C B:GLY225 4.9 15.8 1.0
NH2 B:ARG15 4.9 12.5 0.3
CA B:GLY225 5.0 17.2 1.0

Calcium binding site 6 out of 8 in 1hm9

Go back to Calcium Binding Sites List in 1hm9
Calcium binding site 6 out of 8 in the Crystal Structure of S.Pneumoniae N-Acetylglucosamine-1-Phosphate Uridyltransferase, Glmu, Bound to Acetyl Coenzyme A and Udp-N- Acetylglucosamine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of S.Pneumoniae N-Acetylglucosamine-1-Phosphate Uridyltransferase, Glmu, Bound to Acetyl Coenzyme A and Udp-N- Acetylglucosamine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca2902

b:26.2
occ:1.00
 O B:HOH2252 1.8 28.9 1.0
O B:HOH2208 2.3 29.7 1.0
O1A B:UD12500 2.4 19.8 1.0
O B:HOH2216 2.4 40.5 1.0
NH1 B:ARG15 2.7 26.6 0.7
O B:HOH2299 3.4 44.6 1.0
CZ B:ARG15 3.7 21.2 0.7
PA B:UD12500 3.8 21.5 1.0
NH2 B:ARG15 3.9 17.9 0.7
NH2 B:ARG15 4.2 12.5 0.3
O B:HOH2087 4.3 20.8 1.0
O3A B:UD12500 4.5 19.8 1.0
OE1 B:GLU195 4.5 32.2 1.0
O B:HOH2249 4.5 11.4 1.0
OE2 B:GLU195 4.6 34.7 1.0
O5B B:UD12500 4.6 20.6 1.0
O1B B:UD12500 4.6 23.9 1.0
NE2 B:GLN193 4.7 43.3 1.0
O2A B:UD12500 4.7 18.2 1.0
C5 B:UD12500 4.7 20.7 1.0
C6 B:UD12500 4.8 20.4 1.0
NE B:ARG15 4.9 18.9 0.7

Calcium binding site 7 out of 8 in 1hm9

Go back to Calcium Binding Sites List in 1hm9
Calcium binding site 7 out of 8 in the Crystal Structure of S.Pneumoniae N-Acetylglucosamine-1-Phosphate Uridyltransferase, Glmu, Bound to Acetyl Coenzyme A and Udp-N- Acetylglucosamine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Crystal Structure of S.Pneumoniae N-Acetylglucosamine-1-Phosphate Uridyltransferase, Glmu, Bound to Acetyl Coenzyme A and Udp-N- Acetylglucosamine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca2903

b:38.2
occ:1.00
 OD1 B:ASP416 2.4 17.0 1.0
OD2 B:ASP416 2.6 27.1 1.0
O B:HOH2326 2.7 47.2 1.0
CG B:ASP416 2.8 22.4 1.0
OD2 B:ASP398 3.0 30.3 1.0
CG B:ASP398 3.7 23.6 1.0
N B:ASP398 4.0 15.9 1.0
O B:HOH2126 4.1 28.2 1.0
O B:HOH2218 4.2 38.1 1.0
OD1 B:ASP398 4.3 19.2 1.0
CB B:ASP398 4.4 17.3 1.0
CB B:ASP416 4.4 15.3 1.0
CA B:GLY397 4.5 16.9 1.0
O B:HOH2257 4.6 21.7 1.0
C B:GLY397 4.7 18.2 1.0
CA B:ASP398 4.8 15.7 1.0

Calcium binding site 8 out of 8 in 1hm9

Go back to Calcium Binding Sites List in 1hm9
Calcium binding site 8 out of 8 in the Crystal Structure of S.Pneumoniae N-Acetylglucosamine-1-Phosphate Uridyltransferase, Glmu, Bound to Acetyl Coenzyme A and Udp-N- Acetylglucosamine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Crystal Structure of S.Pneumoniae N-Acetylglucosamine-1-Phosphate Uridyltransferase, Glmu, Bound to Acetyl Coenzyme A and Udp-N- Acetylglucosamine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca2904

b:37.2
occ:0.33
 O B:HOH2254 2.2 14.8 1.0
OD1 B:ASN405 2.3 29.4 1.0
CG B:ASN405 3.4 25.3 1.0
ND2 B:ASN405 3.9 26.2 1.0
O B:GLY380 4.1 13.0 1.0
O B:HOH2255 4.4 17.1 1.0
CB B:ASN405 4.7 19.2 1.0
CA B:ASN405 4.8 15.5 1.0
CA B:GLY380 4.9 14.2 1.0
C B:GLY380 5.0 12.5 1.0

Reference:

G.Sulzenbacher, L.Gal, C.Peneff, F.Fassy, Y.Bourne. Crystal Structure of Streptococcus Pneumoniae N-Acetylglucosamine-1-Phosphate Uridyltransferase Bound to Acetyl-Coenzyme A Reveals A Novel Active Site Architecture. J.Biol.Chem. V. 276 11844 2001.
ISSN: ISSN 0021-9258
PubMed: 11118459
DOI: 10.1074/JBC.M011225200
Page generated: Thu Jul 11 10:05:28 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy