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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

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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

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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

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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

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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

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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

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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

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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

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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

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