Atomistry » Manganese » PDB 3q7c-3rl4 » 3qxb
Atomistry »
  Manganese »
    PDB 3q7c-3rl4 »
      3qxb »

Manganese in PDB 3qxb: Crystal Structure of A Putative Xylose Isomerase (YP_426450.1) From Rhodospirillum Rubrum Atcc 11170 at 1.90 A Resolution

Protein crystallography data

The structure of Crystal Structure of A Putative Xylose Isomerase (YP_426450.1) From Rhodospirillum Rubrum Atcc 11170 at 1.90 A Resolution, PDB code: 3qxb was solved by Joint Center For Structural Genomics (Jcsg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.68 / 1.90
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 76.188, 94.903, 173.197, 90.00, 93.04, 90.00
R / Rfree (%) 15 / 19.2

Other elements in 3qxb:

The structure of Crystal Structure of A Putative Xylose Isomerase (YP_426450.1) From Rhodospirillum Rubrum Atcc 11170 at 1.90 A Resolution also contains other interesting chemical elements:

Iron (Fe) 8 atoms
Chlorine (Cl) 5 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of A Putative Xylose Isomerase (YP_426450.1) From Rhodospirillum Rubrum Atcc 11170 at 1.90 A Resolution (pdb code 3qxb). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 8 binding sites of Manganese where determined in the Crystal Structure of A Putative Xylose Isomerase (YP_426450.1) From Rhodospirillum Rubrum Atcc 11170 at 1.90 A Resolution, PDB code: 3qxb:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Manganese binding site 1 out of 8 in 3qxb

Go back to Manganese Binding Sites List in 3qxb
Manganese binding site 1 out of 8 in the Crystal Structure of A Putative Xylose Isomerase (YP_426450.1) From Rhodospirillum Rubrum Atcc 11170 at 1.90 A Resolution


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of A Putative Xylose Isomerase (YP_426450.1) From Rhodospirillum Rubrum Atcc 11170 at 1.90 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn302

b:25.2
occ:0.34
 FE A:FE301 0.0 26.7 0.7
OE1 A:GLU267 2.1 27.5 1.0
OE2 A:GLU159 2.2 20.9 1.0
OD2 A:ASP194 2.2 26.5 1.0
ND1 A:HIS225 2.3 19.6 1.0
O A:HOH617 2.3 28.8 1.0
O A:HOH507 2.3 23.0 1.0
CD A:GLU267 3.1 29.0 1.0
CE1 A:HIS225 3.1 23.1 1.0
CD A:GLU159 3.1 20.7 1.0
CG A:ASP194 3.2 25.6 1.0
CG A:HIS225 3.3 22.2 1.0
OE1 A:GLU159 3.4 25.9 1.0
OE2 A:GLU267 3.4 31.6 1.0
CB A:ASP194 3.6 25.7 1.0
CB A:HIS225 3.7 22.9 1.0
CE1 A:HIS197 4.0 25.7 1.0
CE1 A:HIS236 4.0 23.3 1.0
MN A:MN303 4.1 31.4 0.5
FE A:FE304 4.1 31.1 0.2
NE2 A:HIS197 4.1 24.9 1.0
NE2 A:HIS225 4.3 21.2 1.0
O A:HOH1078 4.3 35.4 1.0
OD1 A:ASP194 4.4 28.7 1.0
CD2 A:HIS225 4.4 20.8 1.0
CG A:GLU267 4.4 25.1 1.0
CG A:GLU159 4.5 22.0 1.0
NE2 A:HIS236 4.7 24.7 1.0
CB A:GLU267 4.7 22.4 1.0
ND1 A:HIS197 4.8 23.6 1.0
CA A:ASP194 4.9 26.1 1.0
O A:HOH1043 4.9 37.9 1.0
ND1 A:HIS236 5.0 23.7 1.0

Manganese binding site 2 out of 8 in 3qxb

Go back to Manganese Binding Sites List in 3qxb
Manganese binding site 2 out of 8 in the Crystal Structure of A Putative Xylose Isomerase (YP_426450.1) From Rhodospirillum Rubrum Atcc 11170 at 1.90 A Resolution


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of A Putative Xylose Isomerase (YP_426450.1) From Rhodospirillum Rubrum Atcc 11170 at 1.90 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn303

b:31.4
occ:0.50
 FE A:FE304 0.0 31.1 0.2
OD2 A:ASP234 2.0 27.4 1.0
NE2 A:HIS236 2.1 24.7 1.0
NE2 A:HIS197 2.2 24.9 1.0
O A:HOH507 2.3 23.0 1.0
O A:HOH1291 2.4 50.1 1.0
CE1 A:HIS236 2.8 23.3 1.0
CG A:ASP234 3.0 27.9 1.0
CD2 A:HIS197 3.1 25.4 1.0
CE1 A:HIS197 3.2 25.7 1.0
OD1 A:ASP234 3.3 24.6 1.0
CD2 A:HIS236 3.3 22.1 1.0
OD2 A:ASP194 3.8 26.5 1.0
O A:HOH1078 3.9 35.4 1.0
ND1 A:HIS236 4.0 23.7 1.0
MN A:MN302 4.1 25.2 0.3
FE A:FE301 4.1 26.7 0.7
ND1 A:HIS197 4.3 23.6 1.0
CG A:HIS197 4.3 24.0 1.0
NE2 A:GLN227 4.3 24.8 1.0
CG A:HIS236 4.3 24.4 1.0
CB A:ASP234 4.3 29.5 1.0
O B:HOH898 4.4 36.3 1.0
O A:HOH601 4.5 27.1 1.0
CG A:ASP194 4.6 25.6 1.0
OE1 A:GLU267 4.6 27.5 1.0
OE2 A:GLU159 4.8 20.9 1.0

Manganese binding site 3 out of 8 in 3qxb

Go back to Manganese Binding Sites List in 3qxb
Manganese binding site 3 out of 8 in the Crystal Structure of A Putative Xylose Isomerase (YP_426450.1) From Rhodospirillum Rubrum Atcc 11170 at 1.90 A Resolution


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Crystal Structure of A Putative Xylose Isomerase (YP_426450.1) From Rhodospirillum Rubrum Atcc 11170 at 1.90 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn302

b:22.4
occ:0.34
 FE B:FE301 0.0 23.0 0.7
OE2 B:GLU159 2.1 20.8 1.0
OD2 B:ASP194 2.1 20.6 1.0
OE1 B:GLU267 2.2 23.6 1.0
ND1 B:HIS225 2.2 16.4 1.0
O B:HOH468 2.3 21.9 1.0
O B:HOH495 2.4 23.1 1.0
CE1 B:HIS225 3.0 18.3 1.0
CD B:GLU159 3.1 22.7 1.0
CD B:GLU267 3.1 26.5 1.0
CG B:ASP194 3.2 20.4 1.0
CG B:HIS225 3.3 22.3 1.0
OE2 B:GLU267 3.4 31.7 1.0
OE1 B:GLU159 3.4 25.1 1.0
CB B:ASP194 3.6 18.4 1.0
CB B:HIS225 3.8 22.0 1.0
CE1 B:HIS236 3.9 23.5 1.0
CE1 B:HIS197 4.0 22.0 1.0
FE B:FE304 4.1 30.0 0.2
MN B:MN303 4.1 30.1 0.5
O B:HOH1234 4.1 41.8 1.0
NE2 B:HIS197 4.1 19.3 1.0
NE2 B:HIS225 4.2 21.4 1.0
OD1 B:ASP194 4.3 25.5 1.0
CD2 B:HIS225 4.4 19.3 1.0
CG B:GLU159 4.4 20.8 1.0
CG B:GLU267 4.5 23.1 1.0
NE2 B:HIS236 4.6 24.6 1.0
ND1 B:HIS197 4.8 20.4 1.0
CB B:GLU267 4.8 22.1 1.0
CA B:ASP194 4.9 20.1 1.0
CD2 B:HIS197 4.9 20.2 1.0
ND1 B:HIS236 5.0 23.2 1.0

Manganese binding site 4 out of 8 in 3qxb

Go back to Manganese Binding Sites List in 3qxb
Manganese binding site 4 out of 8 in the Crystal Structure of A Putative Xylose Isomerase (YP_426450.1) From Rhodospirillum Rubrum Atcc 11170 at 1.90 A Resolution


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Crystal Structure of A Putative Xylose Isomerase (YP_426450.1) From Rhodospirillum Rubrum Atcc 11170 at 1.90 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn303

b:30.1
occ:0.50
 FE B:FE304 0.0 30.0 0.2
OD2 B:ASP234 1.9 24.6 1.0
NE2 B:HIS197 2.2 19.3 1.0
NE2 B:HIS236 2.2 24.6 1.0
O B:HOH468 2.2 21.9 1.0
O B:HOH1118 2.5 34.8 1.0
CG B:ASP234 2.8 26.1 1.0
CE1 B:HIS236 3.0 23.5 1.0
OD1 B:ASP234 3.1 22.7 1.0
CE1 B:HIS197 3.1 22.0 1.0
CD2 B:HIS197 3.2 20.2 1.0
CD2 B:HIS236 3.4 23.3 1.0
O B:HOH1234 3.7 41.8 1.0
OD2 B:ASP194 3.8 20.6 1.0
FE B:FE301 4.1 23.0 0.7
MN B:MN302 4.1 22.4 0.3
CB B:ASP234 4.1 26.5 1.0
ND1 B:HIS236 4.2 23.2 1.0
ND1 B:HIS197 4.3 20.4 1.0
CG B:HIS197 4.3 21.0 1.0
NE2 B:GLN227 4.3 21.0 1.0
CG B:HIS236 4.4 22.5 1.0
O B:HOH703 4.4 26.8 1.0
O A:HOH1130 4.5 37.4 1.0
CG B:ASP194 4.6 20.4 1.0
OE1 B:GLU267 4.7 23.6 1.0
OE2 B:GLU159 4.8 20.8 1.0

Manganese binding site 5 out of 8 in 3qxb

Go back to Manganese Binding Sites List in 3qxb
Manganese binding site 5 out of 8 in the Crystal Structure of A Putative Xylose Isomerase (YP_426450.1) From Rhodospirillum Rubrum Atcc 11170 at 1.90 A Resolution


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Crystal Structure of A Putative Xylose Isomerase (YP_426450.1) From Rhodospirillum Rubrum Atcc 11170 at 1.90 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn302

b:23.8
occ:0.34
 FE C:FE301 0.0 23.0 0.7
OD2 C:ASP194 2.1 21.7 1.0
OE2 C:GLU159 2.1 20.9 1.0
OE1 C:GLU267 2.1 25.4 1.0
ND1 C:HIS225 2.2 16.2 1.0
O C:HOH718 2.3 24.7 1.0
O C:HOH684 2.5 26.8 1.0
CE1 C:HIS225 3.0 18.9 1.0
CD C:GLU159 3.1 22.8 1.0
CD C:GLU267 3.1 29.7 1.0
CG C:ASP194 3.2 24.1 1.0
CG C:HIS225 3.3 17.4 1.0
OE2 C:GLU267 3.5 33.1 1.0
OE1 C:GLU159 3.5 23.9 1.0
CB C:ASP194 3.6 21.3 1.0
CB C:HIS225 3.7 18.7 1.0
CE1 C:HIS236 3.9 20.6 1.0
CE1 C:HIS197 4.0 23.0 1.0
FE C:FE304 4.1 26.5 0.2
MN C:MN303 4.2 26.3 0.5
NE2 C:HIS225 4.2 17.1 1.0
O C:HOH1187 4.2 38.1 1.0
NE2 C:HIS197 4.2 20.0 1.0
OD1 C:ASP194 4.3 26.4 1.0
CD2 C:HIS225 4.3 15.3 1.0
CG C:GLU159 4.4 20.0 1.0
CG C:GLU267 4.5 22.8 1.0
NE2 C:HIS236 4.6 17.2 1.0
ND1 C:HIS197 4.7 19.4 1.0
CB C:GLU267 4.8 21.1 1.0
CA C:ASP194 4.8 21.0 1.0
CD2 C:LEU192 4.9 23.6 1.0
O C:HOH1245 5.0 43.6 1.0

Manganese binding site 6 out of 8 in 3qxb

Go back to Manganese Binding Sites List in 3qxb
Manganese binding site 6 out of 8 in the Crystal Structure of A Putative Xylose Isomerase (YP_426450.1) From Rhodospirillum Rubrum Atcc 11170 at 1.90 A Resolution


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Crystal Structure of A Putative Xylose Isomerase (YP_426450.1) From Rhodospirillum Rubrum Atcc 11170 at 1.90 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn303

b:26.3
occ:0.50
 FE C:FE304 0.0 26.5 0.2
OD2 C:ASP234 1.9 25.3 1.0
NE2 C:HIS197 2.1 20.0 1.0
NE2 C:HIS236 2.2 17.2 1.0
O C:HOH718 2.2 24.7 1.0
O C:HOH1224 2.8 43.8 1.0
CG C:ASP234 2.9 24.8 1.0
CE1 C:HIS236 3.0 20.6 1.0
CE1 C:HIS197 3.1 23.0 1.0
CD2 C:HIS197 3.1 20.3 1.0
OD1 C:ASP234 3.2 24.8 1.0
CD2 C:HIS236 3.3 21.5 1.0
OD2 C:ASP194 3.9 21.7 1.0
O C:HOH1187 4.0 38.1 1.0
MN C:MN302 4.2 23.8 0.3
FE C:FE301 4.2 23.0 0.7
ND1 C:HIS197 4.2 19.4 1.0
ND1 C:HIS236 4.2 19.8 1.0
CG C:HIS197 4.2 20.7 1.0
CB C:ASP234 4.3 24.1 1.0
NE2 C:GLN227 4.3 17.3 1.0
O D:HOH1128 4.3 33.7 1.0
CG C:HIS236 4.3 20.0 1.0
O C:HOH554 4.5 22.1 1.0
CG C:ASP194 4.5 24.1 1.0
OE1 C:GLU267 4.6 25.4 1.0
OE2 C:GLU159 4.8 20.9 1.0
OD1 C:ASP194 4.8 26.4 1.0

Manganese binding site 7 out of 8 in 3qxb

Go back to Manganese Binding Sites List in 3qxb
Manganese binding site 7 out of 8 in the Crystal Structure of A Putative Xylose Isomerase (YP_426450.1) From Rhodospirillum Rubrum Atcc 11170 at 1.90 A Resolution


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of Crystal Structure of A Putative Xylose Isomerase (YP_426450.1) From Rhodospirillum Rubrum Atcc 11170 at 1.90 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn302

b:26.5
occ:0.34
 FE D:FE301 0.0 26.4 0.7
OE1 D:GLU267 2.2 28.8 1.0
OE2 D:GLU159 2.2 20.3 1.0
OD2 D:ASP194 2.2 22.9 1.0
O D:HOH655 2.3 26.8 1.0
ND1 D:HIS225 2.4 19.1 1.0
O D:HOH967 2.5 29.8 1.0
CD D:GLU159 3.1 21.2 1.0
CD D:GLU267 3.1 29.9 1.0
CE1 D:HIS225 3.2 22.7 1.0
CG D:ASP194 3.2 23.7 1.0
OE1 D:GLU159 3.3 24.4 1.0
OE2 D:GLU267 3.3 36.1 1.0
CG D:HIS225 3.4 22.5 1.0
CB D:ASP194 3.6 21.8 1.0
CB D:HIS225 3.8 23.4 1.0
CE1 D:HIS236 3.9 23.7 1.0
CE1 D:HIS197 4.0 21.6 1.0
NE2 D:HIS197 4.1 20.8 1.0
FE D:FE304 4.2 27.4 0.2
MN D:MN303 4.2 28.1 0.5
NE2 D:HIS225 4.3 21.1 1.0
OD1 D:ASP194 4.4 22.1 1.0
CG D:GLU159 4.4 21.2 1.0
CD2 D:HIS225 4.5 21.7 1.0
CG D:GLU267 4.5 25.7 1.0
O D:HOH1212 4.5 41.0 1.0
NE2 D:HIS236 4.5 27.2 1.0
O D:HOH1272 4.7 41.5 1.0
ND1 D:HIS197 4.7 23.9 1.0
CB D:GLU267 4.8 24.9 1.0
CA D:ASP194 4.9 24.2 1.0
CD2 D:LEU192 4.9 22.4 1.0
CD2 D:HIS197 5.0 24.1 1.0

Manganese binding site 8 out of 8 in 3qxb

Go back to Manganese Binding Sites List in 3qxb
Manganese binding site 8 out of 8 in the Crystal Structure of A Putative Xylose Isomerase (YP_426450.1) From Rhodospirillum Rubrum Atcc 11170 at 1.90 A Resolution


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of Crystal Structure of A Putative Xylose Isomerase (YP_426450.1) From Rhodospirillum Rubrum Atcc 11170 at 1.90 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn303

b:28.1
occ:0.50
 FE D:FE304 0.0 27.4 0.2
OD2 D:ASP234 2.1 23.7 1.0
NE2 D:HIS197 2.2 20.8 1.0
NE2 D:HIS236 2.2 27.2 1.0
O D:HOH655 2.3 26.8 1.0
O D:HOH1237 2.7 43.5 1.0
O D:HOH1279 2.7 47.4 1.0
CG D:ASP234 2.9 26.8 1.0
CE1 D:HIS236 3.1 23.7 1.0
CD2 D:HIS197 3.1 24.1 1.0
OD1 D:ASP234 3.1 22.0 1.0
CE1 D:HIS197 3.2 21.6 1.0
CD2 D:HIS236 3.2 26.3 1.0
OD2 D:ASP194 3.8 22.9 1.0
O D:HOH1272 4.0 41.5 1.0
O D:HOH1212 4.1 41.0 1.0
NE2 D:GLN227 4.2 22.2 1.0
MN D:MN302 4.2 26.5 0.3
FE D:FE301 4.2 26.4 0.7
ND1 D:HIS236 4.2 25.2 1.0
CG D:HIS197 4.3 22.5 1.0
O D:HOH987 4.3 33.7 1.0
ND1 D:HIS197 4.3 23.9 1.0
CB D:ASP234 4.3 25.9 1.0
CG D:HIS236 4.3 24.8 1.0
O D:HOH746 4.4 27.3 1.0
CG D:ASP194 4.6 23.7 1.0
O D:HOH1308 4.7 49.1 1.0
OE1 D:GLU267 4.8 28.8 1.0
OE2 D:GLU159 4.9 20.3 1.0
OD1 D:ASP194 5.0 22.1 1.0

Reference:

Joint Center For Structural Genomics (Jcsg), Joint Center For Structural Genomics (Jcsg). N/A N/A.
Page generated: Sat Oct 5 17:42:51 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy