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Magnesium in PDB 3u3h: X-Ray Crystallographic Analysis of D-Xylose Isomerase-Catalyzed Isomerization of (R)-Glyceraldehyde

Enzymatic activity of X-Ray Crystallographic Analysis of D-Xylose Isomerase-Catalyzed Isomerization of (R)-Glyceraldehyde

All present enzymatic activity of X-Ray Crystallographic Analysis of D-Xylose Isomerase-Catalyzed Isomerization of (R)-Glyceraldehyde:
5.3.1.5;

Protein crystallography data

The structure of X-Ray Crystallographic Analysis of D-Xylose Isomerase-Catalyzed Isomerization of (R)-Glyceraldehyde, PDB code: 3u3h was solved by K.N.Allen, N.R.Silvaggi, M.M.Toteva, J.P.Richard, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.97 / 0.97
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 92.651, 98.148, 102.597, 90.00, 90.00, 90.00
R / Rfree (%) 11.6 / 12.5

Magnesium Binding Sites:

The binding sites of Magnesium atom in the X-Ray Crystallographic Analysis of D-Xylose Isomerase-Catalyzed Isomerization of (R)-Glyceraldehyde (pdb code 3u3h). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the X-Ray Crystallographic Analysis of D-Xylose Isomerase-Catalyzed Isomerization of (R)-Glyceraldehyde, PDB code: 3u3h:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 3u3h

Go back to Magnesium Binding Sites List in 3u3h
Magnesium binding site 1 out of 4 in the X-Ray Crystallographic Analysis of D-Xylose Isomerase-Catalyzed Isomerization of (R)-Glyceraldehyde


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of X-Ray Crystallographic Analysis of D-Xylose Isomerase-Catalyzed Isomerization of (R)-Glyceraldehyde within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg500

b:7.8
occ:0.98
 OE1 A:GLU217 2.0 11.7 1.0
OE2 A:GLU181 2.1 9.4 1.0
OD2 A:ASP245 2.1 9.7 1.0
OD2 A:ASP287 2.1 10.2 1.0
O2 A:03W400 2.1 6.2 0.5
O1 A:03W400 2.2 8.9 0.5
O1 A:FMT401 2.3 7.8 0.5
C1 A:03W400 2.9 8.5 0.5
C2 A:03W400 3.0 7.7 0.5
CD A:GLU181 3.0 8.9 1.0
CG A:ASP287 3.2 8.0 1.0
CD A:GLU217 3.3 8.6 1.0
CG A:ASP245 3.3 7.9 1.0
OE1 A:GLU181 3.3 10.3 1.0
O5 A:03W400 3.4 9.2 0.5
C A:FMT401 3.5 8.6 0.5
HB2 A:GLU217 3.5 8.3 1.0
HB3 A:ASP287 3.5 9.1 1.0
HB2 A:ASP287 3.7 9.1 1.0
MG A:MG501 3.7 3.6 0.4
CB A:ASP287 3.7 7.6 1.0
HB3 A:ASP245 3.7 9.0 1.0
HE1 A:HIS220 3.7 11.4 1.0
H A:FMT401 3.9 10.3 0.5
CB A:ASP245 3.9 7.5 1.0
HB2 A:ASP245 3.9 9.0 1.0
O A:HOH1093 4.0 11.4 1.0
OE2 A:GLU217 4.0 10.5 1.0
O A:HOH1000 4.1 15.0 1.0
CE1 A:HIS220 4.2 9.5 1.0
CG A:GLU217 4.2 7.0 1.0
OD1 A:ASP245 4.2 8.5 1.0
OD1 A:ASP287 4.3 8.6 1.0
CB A:GLU217 4.3 6.9 1.0
C3 A:03W400 4.3 8.2 0.5
HG3 A:GLU217 4.4 8.4 1.0
CG A:GLU181 4.4 8.2 1.0
NE2 A:HIS220 4.4 9.7 1.0
HD22 A:ASN215 4.4 10.7 1.0
O2 A:FMT401 4.5 8.8 0.5
HZ2 A:TRP16 4.5 10.0 1.0
HB3 A:GLU217 4.6 8.3 1.0
HD21 A:ASN215 4.6 10.7 1.0
HG2 A:GLU181 4.6 9.8 1.0
HG3 A:GLU181 4.6 9.8 1.0
ND2 A:ASN215 4.8 8.9 1.0
MG A:MG501 4.9 13.7 0.4

Magnesium binding site 2 out of 4 in 3u3h

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Magnesium binding site 2 out of 4 in the X-Ray Crystallographic Analysis of D-Xylose Isomerase-Catalyzed Isomerization of (R)-Glyceraldehyde


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of X-Ray Crystallographic Analysis of D-Xylose Isomerase-Catalyzed Isomerization of (R)-Glyceraldehyde within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg501

b:11.1
occ:0.26
 MG A:MG501 0.0 11.1 0.3
MG A:MG501 0.7 13.7 0.4
MG A:MG501 1.6 3.6 0.4
OD2 A:ASP255 2.1 13.0 0.5
OE2 A:GLU217 2.2 10.5 1.0
OD1 A:ASP255 2.2 12.5 0.5
CG A:ASP255 2.4 11.6 0.5
OD1 A:ASP257 2.5 15.7 1.0
O A:HOH1000 2.6 15.0 1.0
O A:HOH1329 2.8 19.1 1.0
NE2 A:HIS220 2.8 9.7 1.0
HD2 A:HIS220 2.9 9.9 1.0
HB2 A:ASP255 3.0 11.2 0.5
CD2 A:HIS220 3.2 8.3 1.0
CD A:GLU217 3.3 8.6 1.0
O2 A:FMT401 3.3 8.8 0.5
OD2 A:ASP255 3.4 9.1 0.5
CG A:ASP257 3.4 12.3 1.0
HD22 A:ASN247 3.5 8.8 1.0
OD2 A:ASP257 3.5 14.0 1.0
HE3 A:LYS183 3.6 12.8 1.0
CB A:ASP255 3.8 9.4 0.5
HZ2 A:LYS183 3.8 12.6 1.0
O1 A:FMT401 3.8 7.8 0.5
OE1 A:GLU217 3.8 11.7 1.0
HB3 A:ASP255 3.9 11.2 0.5
CB A:ASP255 3.9 10.5 0.5
C A:FMT401 3.9 8.6 0.5
HZ1 A:LYS183 4.0 12.6 1.0
CE1 A:HIS220 4.1 9.5 1.0
CG A:ASP255 4.1 9.6 0.5
HD21 A:ASN247 4.1 8.8 1.0
ND2 A:ASN247 4.1 7.3 1.0
NZ A:LYS183 4.2 10.5 1.0
HB2 A:ASP255 4.3 12.6 0.5
HB3 A:ASP255 4.3 12.6 0.5
HG2 A:GLU217 4.3 8.4 1.0
CE A:LYS183 4.4 10.6 1.0
O A:HOH1053 4.4 11.5 1.0
O A:HOH471 4.4 34.0 1.0
CG A:GLU217 4.4 7.0 1.0
CG A:HIS220 4.5 7.3 1.0
HE1 A:HIS220 4.5 11.4 1.0
O1 A:03W400 4.5 8.9 0.5
HD2 A:LYS183 4.8 11.1 1.0
HA A:ASP255 4.8 11.8 0.5
CB A:ASP257 4.8 9.6 1.0
H A:ASP257 4.9 9.3 1.0
HA A:ASP257 4.9 9.8 1.0
CA A:ASP255 4.9 9.8 0.5
ND1 A:HIS220 4.9 8.6 1.0

Magnesium binding site 3 out of 4 in 3u3h

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Magnesium binding site 3 out of 4 in the X-Ray Crystallographic Analysis of D-Xylose Isomerase-Catalyzed Isomerization of (R)-Glyceraldehyde


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of X-Ray Crystallographic Analysis of D-Xylose Isomerase-Catalyzed Isomerization of (R)-Glyceraldehyde within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg501

b:13.7
occ:0.38
 MG A:MG501 0.0 13.7 0.4
MG A:MG501 0.7 11.1 0.3
MG A:MG501 1.5 3.6 0.4
O A:HOH1000 2.0 15.0 1.0
OE2 A:GLU217 2.1 10.5 1.0
OD1 A:ASP257 2.3 15.7 1.0
OD2 A:ASP255 2.4 13.0 0.5
OD1 A:ASP255 2.7 12.5 0.5
CG A:ASP255 2.9 11.6 0.5
CG A:ASP257 3.0 12.3 1.0
OD2 A:ASP257 3.0 14.0 1.0
O A:HOH1329 3.1 19.1 1.0
CD A:GLU217 3.2 8.6 1.0
NE2 A:HIS220 3.2 9.7 1.0
O2 A:FMT401 3.3 8.8 0.5
HD22 A:ASN247 3.3 8.8 1.0
HB2 A:ASP255 3.4 11.2 0.5
HD2 A:HIS220 3.4 9.9 1.0
O1 A:FMT401 3.6 7.8 0.5
OE1 A:GLU217 3.6 11.7 1.0
CD2 A:HIS220 3.7 8.3 1.0
OD2 A:ASP255 3.7 9.1 0.5
HD21 A:ASN247 3.7 8.8 1.0
C A:FMT401 3.8 8.6 0.5
ND2 A:ASN247 3.9 7.3 1.0
HZ2 A:LYS183 4.1 12.6 1.0
CB A:ASP255 4.2 9.4 0.5
HE3 A:LYS183 4.2 12.8 1.0
O A:HOH471 4.2 34.0 1.0
O1 A:03W400 4.3 8.9 0.5
HZ1 A:LYS183 4.3 12.6 1.0
CB A:ASP255 4.4 10.5 0.5
CE1 A:HIS220 4.4 9.5 1.0
HG2 A:GLU217 4.4 8.4 1.0
HB3 A:ASP255 4.4 11.2 0.5
CG A:GLU217 4.4 7.0 1.0
CB A:ASP257 4.5 9.6 1.0
CG A:ASP255 4.5 9.6 0.5
NZ A:LYS183 4.6 10.5 1.0
O A:HOH1053 4.6 11.5 1.0
HZ3 A:LYS289 4.6 28.5 1.0
HA A:ASP257 4.6 9.8 1.0
HB3 A:ASP255 4.6 12.6 0.5
HE1 A:HIS220 4.7 11.4 1.0
OD2 A:ASP287 4.7 10.2 1.0
HB2 A:ASP255 4.8 12.6 0.5
HB3 A:ASP257 4.8 11.5 1.0
H A:ASP257 4.9 9.3 1.0
MG A:MG500 4.9 7.8 1.0
O A:ASP287 4.9 7.9 1.0
CE A:LYS183 4.9 10.6 1.0
H A:FMT401 4.9 10.3 0.5
HG3 A:GLU217 5.0 8.4 1.0
CG A:ASP287 5.0 8.0 1.0
CG A:HIS220 5.0 7.3 1.0

Magnesium binding site 4 out of 4 in 3u3h

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Magnesium binding site 4 out of 4 in the X-Ray Crystallographic Analysis of D-Xylose Isomerase-Catalyzed Isomerization of (R)-Glyceraldehyde


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of X-Ray Crystallographic Analysis of D-Xylose Isomerase-Catalyzed Isomerization of (R)-Glyceraldehyde within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg501

b:3.6
occ:0.36
 MG A:MG501 0.0 3.6 0.4
MG A:MG501 1.5 13.7 0.4
MG A:MG501 1.6 11.1 0.3
O A:HOH1000 2.1 15.0 1.0
OE2 A:GLU217 2.1 10.5 1.0
NE2 A:HIS220 2.2 9.7 1.0
O1 A:FMT401 2.2 7.8 0.5
O2 A:FMT401 2.3 8.8 0.5
C A:FMT401 2.5 8.6 0.5
CD A:GLU217 2.7 8.6 1.0
OE1 A:GLU217 2.7 11.7 1.0
O1 A:03W400 3.0 8.9 0.5
CE1 A:HIS220 3.1 9.5 1.0
OD2 A:ASP255 3.1 13.0 0.5
CD2 A:HIS220 3.1 8.3 1.0
HE1 A:HIS220 3.3 11.4 1.0
HD2 A:HIS220 3.3 9.9 1.0
HZ2 A:LYS183 3.5 12.6 1.0
H A:FMT401 3.6 10.3 0.5
MG A:MG500 3.7 7.8 1.0
OD1 A:ASP255 3.7 12.5 0.5
OD1 A:ASP257 3.8 15.7 1.0
CG A:ASP255 3.8 11.6 0.5
O A:HOH1329 3.9 19.1 1.0
HE3 A:LYS183 3.9 12.8 1.0
OD2 A:ASP287 4.1 10.2 1.0
CG A:GLU217 4.1 7.0 1.0
HD22 A:ASN247 4.1 8.8 1.0
NZ A:LYS183 4.2 10.5 1.0
C1 A:03W400 4.2 8.5 0.5
ND1 A:HIS220 4.2 8.6 1.0
OD2 A:ASP257 4.2 14.0 1.0
CG A:HIS220 4.2 7.3 1.0
HD2 A:LYS183 4.2 11.1 1.0
HZ1 A:LYS183 4.3 12.6 1.0
OD2 A:ASP255 4.3 9.1 0.5
HG2 A:GLU217 4.3 8.4 1.0
OE2 A:GLU181 4.3 9.4 1.0
CG A:ASP257 4.4 12.3 1.0
HB2 A:ASP255 4.5 11.2 0.5
CE A:LYS183 4.5 10.6 1.0
O5 A:03W400 4.5 9.2 0.5
HB3 A:GLU217 4.6 8.3 1.0
HD21 A:ASN247 4.6 8.8 1.0
CG A:ASP287 4.7 8.0 1.0
ND2 A:ASN247 4.7 7.3 1.0
HG3 A:GLU217 4.7 8.4 1.0
HB2 A:GLU217 4.7 8.3 1.0
CB A:GLU217 4.8 6.9 1.0
O A:HOH431 4.8 34.9 1.0
CD A:LYS183 4.9 9.2 1.0
HZ3 A:LYS183 4.9 12.6 1.0

Reference:

M.M.Toteva, N.R.Silvaggi, K.N.Allen, J.P.Richard. Binding Energy and Catalysis By D-Xylose Isomerase: Kinetic, Product, and X-Ray Crystallographic Analysis of Enzyme-Catalyzed Isomerization of (R)-Glyceraldehyde. Biochemistry V. 50 10170 2011.
ISSN: ISSN 0006-2960
PubMed: 21995300
DOI: 10.1021/BI201378C
Page generated: Thu Aug 15 12:20:18 2024

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