Atomistry » Magnesium » PDB 1tkk-1u3f » 1tmm
Atomistry »
  Magnesium »
    PDB 1tkk-1u3f »
      1tmm »

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

Go back to Magnesium Binding Sites List in 1tmm
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

Go back to Magnesium Binding Sites List in 1tmm
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

Go back to Magnesium Binding Sites List in 1tmm
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

Go back to Magnesium Binding Sites List in 1tmm
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: Mon Dec 14 06:51:41 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy