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Magnesium in PDB 1tmm: Crystal Structure of Ternary Complex of E.Coli Hppk(W89A) with Mgampcpp and 6-Hydroxymethylpterin

Enzymatic activity of Crystal Structure of Ternary Complex of E.Coli Hppk(W89A) with Mgampcpp and 6-Hydroxymethylpterin

All present enzymatic activity of Crystal Structure of Ternary Complex of E.Coli Hppk(W89A) with Mgampcpp and 6-Hydroxymethylpterin:
2.7.6.3;

Protein crystallography data

The structure of Crystal Structure of Ternary Complex of E.Coli Hppk(W89A) with Mgampcpp and 6-Hydroxymethylpterin, PDB code: 1tmm was solved by J.Blaszczyk, Y.Li, Y.Wu, G.Shi, X.Ji, H.Yan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 1.25
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 47.992, 47.392, 71.438, 90.00, 104.13, 90.00
R / Rfree (%) 13.2 / 16.4

Other elements in 1tmm:

The structure of Crystal Structure of Ternary Complex of E.Coli Hppk(W89A) with Mgampcpp and 6-Hydroxymethylpterin also contains other interesting chemical elements:

Chlorine (Cl) 3 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Ternary Complex of E.Coli Hppk(W89A) with Mgampcpp and 6-Hydroxymethylpterin (pdb code 1tmm). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Crystal Structure of Ternary Complex of E.Coli Hppk(W89A) with Mgampcpp and 6-Hydroxymethylpterin, PDB code: 1tmm:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in 1tmm

Go back to Magnesium Binding Sites List in 1tmm
Magnesium binding site 1 out of 5 in the Crystal Structure of Ternary Complex of E.Coli Hppk(W89A) with Mgampcpp and 6-Hydroxymethylpterin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Ternary Complex of E.Coli Hppk(W89A) with Mgampcpp and 6-Hydroxymethylpterin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg161

b:7.8
occ:1.00
 OD1 A:ASP97 2.0 7.6 1.0
OD1 A:ASP95 2.1 7.2 1.0
O A:HOH404 2.1 8.0 1.0
O A:HOH408 2.1 8.3 1.0
O1B A:APC171 2.1 8.8 1.0
O1A A:APC171 2.1 8.7 1.0
CG A:ASP95 3.0 6.7 1.0
CG A:ASP97 3.1 7.0 1.0
PB A:APC171 3.2 9.2 1.0
PA A:APC171 3.2 9.2 1.0
OD2 A:ASP95 3.3 8.5 1.0
C3A A:APC171 3.5 9.4 1.0
MG A:MG162 3.5 8.2 1.0
OD2 A:ASP97 3.6 7.8 1.0
O5' A:APC171 3.8 9.2 1.0
O A:HOH440 3.9 23.1 1.0
O2B A:APC171 4.0 11.1 1.0
NZ A:LYS85 4.0 9.4 1.0
OE2 A:GLU77 4.2 8.7 1.0
O A:LEU96 4.2 7.3 1.0
CB A:ASP95 4.3 7.2 1.0
CB A:ASP97 4.4 6.9 1.0
NH1 A:ARG82 4.4 10.1 1.0
O3B A:APC171 4.5 10.3 1.0
NH2 A:ARG82 4.5 10.6 1.0
O2A A:APC171 4.5 11.1 1.0
C A:LEU96 4.5 6.0 1.0
O1G A:APC171 4.7 12.0 1.0
CA A:ASP97 4.7 6.0 1.0
N A:LEU96 4.7 6.6 1.0
O A:HOH435 4.7 9.2 1.0
O3G A:APC171 4.7 9.6 1.0
CA A:ASP95 4.7 7.1 1.0
O6A A:HHR181 4.7 10.3 1.0
C2 A:APC171 4.8 6.6 1.0
N A:ASP97 4.8 6.3 1.0
N3 A:APC171 4.8 7.3 1.0
PG A:APC171 4.9 9.8 1.0
C A:ASP95 4.9 6.5 1.0
CZ A:ARG82 5.0 9.0 1.0

Magnesium binding site 2 out of 5 in 1tmm

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Magnesium binding site 2 out of 5 in the Crystal Structure of Ternary Complex of E.Coli Hppk(W89A) with Mgampcpp and 6-Hydroxymethylpterin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Ternary Complex of E.Coli Hppk(W89A) with Mgampcpp and 6-Hydroxymethylpterin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg162

b:8.2
occ:1.00
 OD2 A:ASP97 2.0 7.8 1.0
O3G A:APC171 2.0 9.6 1.0
OD2 A:ASP95 2.1 8.5 1.0
O A:HOH496 2.1 8.9 1.0
O1B A:APC171 2.1 8.8 1.0
O6A A:HHR181 2.1 10.3 1.0
CG A:ASP97 3.0 7.0 1.0
CG A:ASP95 3.1 6.7 1.0
PG A:APC171 3.2 9.8 1.0
PB A:APC171 3.2 9.2 1.0
C6A A:HHR181 3.3 10.4 1.0
OD1 A:ASP97 3.3 7.6 1.0
O3B A:APC171 3.4 10.3 1.0
MG A:MG161 3.5 7.8 1.0
OD1 A:ASP95 3.6 7.2 1.0
O1G A:APC171 3.9 12.0 1.0
O2B A:APC171 4.0 11.1 1.0
O A:HOH414 4.0 9.6 1.0
N5 A:HHR181 4.1 9.9 1.0
C6 A:HHR181 4.1 10.6 1.0
NH1 A:ARG121 4.2 9.8 1.0
O A:HOH469 4.2 13.3 1.0
O A:HOH407 4.2 14.3 1.0
CB A:ASP97 4.3 6.9 1.0
O2G A:APC171 4.4 9.7 1.0
CB A:ASP95 4.5 7.2 1.0
O A:HOH440 4.6 23.1 1.0
O A:HOH408 4.6 8.3 1.0
O A:HOH481 4.6 11.5 1.0
C3A A:APC171 4.7 9.4 1.0
NE2 A:HIS115 4.7 9.6 1.0
O1A A:APC171 4.9 8.7 1.0
CE A:MET124 5.0 11.4 1.0

Magnesium binding site 3 out of 5 in 1tmm

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Magnesium binding site 3 out of 5 in the Crystal Structure of Ternary Complex of E.Coli Hppk(W89A) with Mgampcpp and 6-Hydroxymethylpterin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Ternary Complex of E.Coli Hppk(W89A) with Mgampcpp and 6-Hydroxymethylpterin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg163

b:27.6
occ:1.00
 O A:HOH644 2.2 25.9 1.0
O A:SER31 2.3 13.3 1.0
O A:GLY26 2.4 20.1 1.0
O A:HOH567 2.4 22.5 1.0
O A:HOH671 2.6 27.3 1.0
O A:HOH672 2.6 33.7 1.0
O A:HOH935 3.3 47.2 1.0
C A:SER31 3.5 13.0 1.0
C A:GLY26 3.6 15.2 1.0
O A:ILE28 3.8 16.9 1.0
O A:HOH730 4.0 40.8 1.0
CA A:HIS32 4.2 11.8 1.0
N A:HIS32 4.3 10.7 1.0
CB A:HIS32 4.3 13.1 1.0
CA A:ASP27 4.4 16.4 1.0
N A:ASP27 4.4 14.0 1.0
O A:HOH983 4.5 43.9 1.0
N A:SER31 4.5 13.6 1.0
O A:HOH418 4.5 13.9 1.0
CA A:SER31 4.6 12.2 1.0
C A:ASP27 4.6 15.2 1.0
CA A:GLY26 4.6 12.6 1.0
C A:ILE28 4.8 14.6 1.0
N A:ILE28 4.8 13.7 1.0
OXT A:ACT167 4.8 21.8 1.0
O A:HOH819 4.9 42.6 1.0
O A:ASP27 5.0 16.4 1.0

Magnesium binding site 4 out of 5 in 1tmm

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Magnesium binding site 4 out of 5 in the Crystal Structure of Ternary Complex of E.Coli Hppk(W89A) with Mgampcpp and 6-Hydroxymethylpterin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Ternary Complex of E.Coli Hppk(W89A) with Mgampcpp and 6-Hydroxymethylpterin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg361

b:9.1
occ:1.00
 OD1 B:ASP297 2.0 8.6 1.0
O1B B:APC371 2.1 9.0 1.0
O B:HOH431 2.1 8.4 1.0
O1A B:APC371 2.1 9.2 1.0
O B:HOH433 2.1 9.5 1.0
OD1 B:ASP295 2.1 9.0 1.0
CG B:ASP295 3.0 7.9 1.0
CG B:ASP297 3.1 7.8 1.0
PB B:APC371 3.2 10.1 1.0
PA B:APC371 3.2 10.1 1.0
OD2 B:ASP295 3.3 10.1 1.0
C3A B:APC371 3.5 11.0 1.0
MG B:MG362 3.5 9.6 1.0
OD2 B:ASP297 3.6 10.4 1.0
O5' B:APC371 3.8 10.3 1.0
O2B B:APC371 3.9 11.9 1.0
NZ B:LYS285 4.0 8.4 0.9
O B:HOH449 4.1 15.1 1.0
OE2 B:GLU277 4.2 8.7 1.0
O B:LEU296 4.2 8.2 1.0
NH1 B:ARG282 4.3 11.9 1.0
CB B:ASP295 4.4 8.1 1.0
CB B:ASP297 4.4 8.1 1.0
O3B B:APC371 4.5 10.7 1.0
O2A B:APC371 4.5 10.6 1.0
NH2 B:ARG282 4.6 19.1 1.0
C B:LEU296 4.6 7.4 1.0
C2 B:APC371 4.6 7.5 1.0
O B:HOH436 4.7 9.2 1.0
CA B:ASP297 4.7 8.0 1.0
O3G B:APC371 4.7 12.1 1.0
N3 B:APC371 4.7 8.7 1.0
N B:LEU296 4.7 7.2 1.0
CA B:ASP295 4.8 8.2 1.0
O6A B:HHR381 4.8 11.5 1.0
O1G B:APC371 4.8 13.7 1.0
N B:ASP297 4.8 7.0 1.0
CZ B:ARG282 4.9 14.6 1.0
NH1 B:ARG292 5.0 24.4 1.0
C B:ASP295 5.0 7.5 1.0
PG B:APC371 5.0 11.4 1.0

Magnesium binding site 5 out of 5 in 1tmm

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Magnesium binding site 5 out of 5 in the Crystal Structure of Ternary Complex of E.Coli Hppk(W89A) with Mgampcpp and 6-Hydroxymethylpterin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of Ternary Complex of E.Coli Hppk(W89A) with Mgampcpp and 6-Hydroxymethylpterin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg362

b:9.6
occ:1.00
 OD2 B:ASP297 2.0 10.4 1.0
O3G B:APC371 2.0 12.1 1.0
OD2 B:ASP295 2.1 10.1 1.0
O1B B:APC371 2.2 9.0 1.0
O6A B:HHR381 2.2 11.5 1.0
O B:HOH517 2.2 13.1 1.0
CG B:ASP297 2.9 7.8 1.0
CG B:ASP295 3.2 7.9 1.0
PG B:APC371 3.2 11.4 1.0
PB B:APC371 3.2 10.1 1.0
OD1 B:ASP297 3.2 8.6 1.0
O3B B:APC371 3.3 10.7 1.0
C6A B:HHR381 3.4 15.0 1.0
MG B:MG361 3.5 9.1 1.0
OD1 B:ASP295 3.6 9.0 1.0
O1G B:APC371 3.9 13.7 1.0
O2B B:APC371 4.0 11.9 1.0
O B:HOH536 4.0 11.3 1.0
NH1 B:ARG321 4.0 10.9 1.0
O B:HOH499 4.1 31.5 1.0
CB B:ASP297 4.2 8.1 1.0
N5 B:HHR381 4.3 16.7 1.0
C6 B:HHR381 4.3 14.1 1.0
O B:HOH464 4.3 25.8 1.0
NE2 B:HIS315 4.3 9.8 1.0
O2G B:APC371 4.4 11.4 1.0
NH1 B:ARG292 4.4 24.4 1.0
CB B:ASP295 4.5 8.1 1.0
O B:HOH433 4.5 9.5 1.0
O B:HOH449 4.6 15.1 1.0
C3A B:APC371 4.6 11.0 1.0
O B:HOH468 4.7 15.3 1.0
CE B:MET324 4.9 13.9 1.0
O1A B:APC371 4.9 9.2 1.0

Reference:

Y.Li, J.Blaszczyk, Y.Wu, G.Shi, X.Ji, H.Yan. Is the Critical Role of Loop 3 of Escherichia Coli 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase in Catalysis Due to Loop-3 Residues Arginine-84 and Tryptophan-89? Site-Directed Mutagenesis, Biochemical, and Crystallographic Studies. Biochemistry V. 44 8590 2005.
ISSN: ISSN 0006-2960
PubMed: 15952765
DOI: 10.1021/BI0503495
Page generated: Tue Aug 13 14:35:39 2024

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