Atomistry » Zinc » PDB 2ow0-2pcu » 2p2l
Atomistry »
  Zinc »
    PDB 2ow0-2pcu »
      2p2l »

Zinc in PDB 2p2l: RAC1-Gdp-Zinc Complex

Protein crystallography data

The structure of RAC1-Gdp-Zinc Complex, PDB code: 2p2l was solved by G.Prehna, C.E.Stebbins, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 77.62 / 1.90
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 89.727, 89.727, 190.618, 90.00, 90.00, 120.00
R / Rfree (%) 17.6 / 20.8

Zinc Binding Sites:

The binding sites of Zinc atom in the RAC1-Gdp-Zinc Complex (pdb code 2p2l). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the RAC1-Gdp-Zinc Complex, PDB code: 2p2l:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 2p2l

Go back to Zinc Binding Sites List in 2p2l
Zinc binding site 1 out of 8 in the RAC1-Gdp-Zinc Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of RAC1-Gdp-Zinc Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn201

b:26.3
occ:1.00
 O3B A:GDP200 2.1 15.6 1.0
O A:HOH1114 2.1 15.9 1.0
O A:HOH1148 2.1 18.8 1.0
OG1 A:THR17 2.2 25.2 1.0
O A:HOH915 2.2 16.4 1.0
O A:THR35 2.3 26.3 1.0
CB A:THR17 3.2 24.9 1.0
PB A:GDP200 3.3 17.9 1.0
C A:THR35 3.3 26.4 1.0
O1B A:GDP200 3.5 19.4 1.0
N A:THR17 4.0 25.7 1.0
OD2 A:ASP57 4.0 28.1 1.0
O A:PRO34 4.0 24.6 1.0
O2A A:GDP200 4.1 18.4 1.0
CA A:THR35 4.1 25.8 1.0
CA A:THR17 4.2 25.3 1.0
CG2 A:THR17 4.3 25.5 1.0
OD1 A:ASP57 4.3 28.1 1.0
N A:VAL36 4.3 26.2 1.0
O A:HOH1083 4.3 35.5 1.0
O3A A:GDP200 4.4 17.8 1.0
O2B A:GDP200 4.4 15.8 1.0
PA A:GDP200 4.5 18.4 1.0
O A:HOH905 4.5 21.1 1.0
O A:HOH1149 4.5 37.5 1.0
O A:THR58 4.5 31.7 1.0
CG A:ASP57 4.5 28.6 1.0
CA A:VAL36 4.6 26.0 1.0
O1A A:GDP200 4.7 19.9 1.0
C A:PRO34 4.9 25.7 1.0
NZ A:LYS16 4.9 24.1 1.0
O A:HOH965 4.9 27.3 1.0

Zinc binding site 2 out of 8 in 2p2l

Go back to Zinc Binding Sites List in 2p2l
Zinc binding site 2 out of 8 in the RAC1-Gdp-Zinc Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of RAC1-Gdp-Zinc Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn202

b:28.5
occ:1.00
 OD2 A:ASP63 2.0 25.7 1.0
NE2 A:HIS104 2.0 25.9 1.0
OE2 A:GLU100 2.1 26.2 1.0
CG A:ASP63 2.6 25.3 1.0
OD1 A:ASP63 2.7 21.9 1.0
CD A:GLU100 2.8 28.6 1.0
OE1 A:GLU100 2.9 29.6 1.0
CD2 A:HIS104 3.0 25.9 1.0
CE1 A:HIS104 3.0 24.6 1.0
CB A:ASP63 4.1 25.5 1.0
ND1 A:HIS104 4.1 23.8 1.0
CG A:HIS104 4.1 24.7 1.0
NE2 A:GLN61 4.2 29.0 1.0
CG A:GLU100 4.3 26.6 1.0
N A:ASP63 4.3 26.3 1.0
CB A:GLU62 4.6 27.1 1.0
CD2 A:HIS103 4.6 19.6 1.0
CG A:GLN61 4.6 31.9 1.0
CA A:GLU100 4.6 26.9 1.0
CB A:GLU100 4.7 27.1 1.0
CA A:ASP63 4.7 26.1 1.0
O A:HOH968 4.8 27.3 1.0
O A:HOH923 4.8 28.8 1.0
CB A:HIS103 4.9 23.8 1.0
CD A:GLN61 4.9 34.0 1.0
CG A:GLU62 4.9 27.3 1.0
O A:GLU100 5.0 26.8 1.0
CG A:HIS103 5.0 21.2 1.0

Zinc binding site 3 out of 8 in 2p2l

Go back to Zinc Binding Sites List in 2p2l
Zinc binding site 3 out of 8 in the RAC1-Gdp-Zinc Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of RAC1-Gdp-Zinc Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn901

b:28.1
occ:1.00
 OD1 A:ASP38 2.0 23.8 1.0
O A:HOH1125 2.0 19.5 1.0
OD1 B:ASP38 2.0 23.9 1.0
OD1 C:ASP38 2.0 26.1 1.0
CG A:ASP38 2.7 24.9 1.0
CG C:ASP38 2.7 24.8 1.0
OD2 A:ASP38 2.7 24.9 1.0
CG B:ASP38 2.7 21.6 1.0
OD2 C:ASP38 2.7 28.0 1.0
OD2 B:ASP38 2.8 24.9 1.0
O A:HOH1156 3.2 46.0 1.0
O A:HOH989 3.9 26.3 1.0
O B:HOH231 3.9 25.5 1.0
O C:HOH273 4.0 26.4 1.0
CB A:ASP38 4.2 26.0 1.0
CB B:ASP38 4.2 24.1 1.0
CB C:ASP38 4.2 25.3 1.0
O C:HOH207 4.3 19.0 1.0
O B:HOH234 4.3 22.0 1.0
O C:HOH219 4.3 25.7 1.0
O A:HOH1173 4.6 38.9 1.0
O B:HOH251 4.7 36.6 1.0
O B:HOH216 4.7 23.7 1.0
O C:HOH246 4.7 29.0 1.0
O C:HOH264 4.8 40.9 1.0
O A:HOH959 4.8 26.6 1.0

Zinc binding site 4 out of 8 in 2p2l

Go back to Zinc Binding Sites List in 2p2l
Zinc binding site 4 out of 8 in the RAC1-Gdp-Zinc Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of RAC1-Gdp-Zinc Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn902

b:49.1
occ:1.00
 OE2 A:GLU131 2.0 32.0 1.0
OE1 A:GLU127 2.1 32.7 1.0
CD A:GLU131 2.9 32.0 1.0
CD A:GLU127 3.1 31.6 1.0
CG A:GLU131 3.1 32.0 1.0
CG A:GLU127 3.3 29.1 1.0
O A:HOH1136 4.0 55.8 1.0
OE1 A:GLU131 4.1 32.4 1.0
OE2 A:GLU127 4.2 33.8 1.0
NZ A:LYS130 4.3 39.4 1.0
O A:GLU127 4.6 28.5 1.0
CB A:GLU131 4.7 31.4 1.0
CB A:GLU127 4.8 29.3 1.0

Zinc binding site 5 out of 8 in 2p2l

Go back to Zinc Binding Sites List in 2p2l
Zinc binding site 5 out of 8 in the RAC1-Gdp-Zinc Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of RAC1-Gdp-Zinc Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn201

b:28.6
occ:1.00
 O B:HOH431 2.1 17.3 1.0
O B:HOH421 2.1 18.3 1.0
OG1 B:THR17 2.2 26.4 1.0
O3B B:GDP200 2.2 19.6 1.0
O B:HOH412 2.2 19.9 1.0
O B:THR35 2.3 27.9 1.0
CB B:THR17 3.2 26.6 1.0
PB B:GDP200 3.3 20.0 1.0
C B:THR35 3.3 27.8 1.0
O1B B:GDP200 3.5 20.4 1.0
OD2 B:ASP57 3.9 29.1 1.0
N B:THR17 4.0 26.5 1.0
O B:PRO34 4.0 27.0 1.0
CA B:THR35 4.1 27.3 1.0
O2A B:GDP200 4.1 20.4 1.0
CA B:THR17 4.1 26.5 1.0
CG2 B:THR17 4.2 26.2 1.0
OD1 B:ASP57 4.3 29.5 1.0
N B:VAL36 4.3 27.2 1.0
O3A B:GDP200 4.3 20.4 1.0
O2B B:GDP200 4.4 19.4 1.0
O B:HOH327 4.4 34.0 1.0
PA B:GDP200 4.5 21.8 1.0
CG B:ASP57 4.5 29.3 1.0
O B:THR58 4.5 32.3 1.0
CA B:VAL36 4.6 27.6 1.0
O B:HOH205 4.6 23.3 1.0
O B:HOH339 4.7 42.7 1.0
O1A B:GDP200 4.8 22.4 1.0
NZ B:LYS16 4.9 24.4 1.0
C B:PRO34 4.9 27.7 1.0
CB B:LYS16 5.0 27.6 1.0

Zinc binding site 6 out of 8 in 2p2l

Go back to Zinc Binding Sites List in 2p2l
Zinc binding site 6 out of 8 in the RAC1-Gdp-Zinc Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of RAC1-Gdp-Zinc Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn202

b:30.6
occ:1.00
 OD2 B:ASP63 2.0 25.9 1.0
NE2 B:HIS104 2.0 23.5 1.0
OE2 B:GLU100 2.1 27.1 1.0
CG B:ASP63 2.7 25.0 1.0
OD1 B:ASP63 2.8 22.6 1.0
CD B:GLU100 2.8 28.3 1.0
CD2 B:HIS104 2.9 26.6 1.0
OE1 B:GLU100 2.9 30.1 1.0
CE1 B:HIS104 3.0 26.6 1.0
CG B:HIS104 4.1 25.7 1.0
ND1 B:HIS104 4.1 25.0 1.0
CB B:ASP63 4.1 26.5 1.0
NE2 B:GLN61 4.2 28.1 1.0
CG B:GLU100 4.2 27.5 1.0
N B:ASP63 4.3 27.3 1.0
CB B:GLU62 4.5 28.8 1.0
CA B:GLU100 4.6 26.8 1.0
CB B:GLU100 4.7 26.3 1.0
CD2 B:HIS103 4.7 23.5 1.0
CG B:GLN61 4.7 32.1 1.0
CA B:ASP63 4.7 26.8 1.0
CG B:GLU62 4.9 27.4 1.0
O B:HOH305 4.9 38.6 1.0
CB B:HIS103 4.9 24.6 1.0
CD B:GLN61 4.9 33.4 1.0
O B:GLU100 4.9 26.5 1.0

Zinc binding site 7 out of 8 in 2p2l

Go back to Zinc Binding Sites List in 2p2l
Zinc binding site 7 out of 8 in the RAC1-Gdp-Zinc Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of RAC1-Gdp-Zinc Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn201

b:26.9
occ:1.00
 O3B C:GDP200 2.1 18.9 1.0
O C:HOH443 2.1 15.9 1.0
O C:HOH434 2.1 17.3 1.0
OG1 C:THR17 2.2 25.2 1.0
O C:HOH424 2.2 19.3 1.0
O C:THR35 2.2 25.4 1.0
CB C:THR17 3.2 26.7 1.0
PB C:GDP200 3.3 19.3 1.0
C C:THR35 3.3 26.5 1.0
O1B C:GDP200 3.4 19.9 1.0
N C:THR17 4.0 25.4 1.0
OD2 C:ASP57 4.0 26.0 1.0
O C:PRO34 4.0 26.3 1.0
CA C:THR35 4.0 26.2 1.0
O2A C:GDP200 4.1 19.0 1.0
CA C:THR17 4.1 25.8 1.0
CG2 C:THR17 4.2 25.3 1.0
OD1 C:ASP57 4.3 26.4 1.0
N C:VAL36 4.3 26.5 1.0
O3A C:GDP200 4.3 19.7 1.0
O2B C:GDP200 4.3 18.8 1.0
O B:HOH420 4.4 35.0 1.0
PA C:GDP200 4.5 19.2 1.0
O B:HOH330 4.5 33.7 1.0
O C:HOH211 4.5 22.3 1.0
CG C:ASP57 4.6 28.2 1.0
O C:THR58 4.6 30.0 1.0
CA C:VAL36 4.6 26.1 1.0
O1A C:GDP200 4.7 17.9 1.0
NZ C:LYS16 4.8 24.7 1.0
C C:PRO34 4.9 26.3 1.0
CB C:LYS16 5.0 25.2 1.0
O C:HOH209 5.0 25.1 1.0

Zinc binding site 8 out of 8 in 2p2l

Go back to Zinc Binding Sites List in 2p2l
Zinc binding site 8 out of 8 in the RAC1-Gdp-Zinc Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of RAC1-Gdp-Zinc Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn202

b:31.6
occ:1.00
 OD2 C:ASP63 2.0 23.8 1.0
NE2 C:HIS104 2.0 25.4 1.0
OE2 C:GLU100 2.1 27.5 1.0
CG C:ASP63 2.6 24.6 1.0
OD1 C:ASP63 2.7 23.9 1.0
CD C:GLU100 2.8 27.3 1.0
OE1 C:GLU100 2.9 30.1 1.0
CD2 C:HIS104 2.9 26.3 1.0
CE1 C:HIS104 3.0 27.1 1.0
ND1 C:HIS104 4.1 26.6 1.0
CG C:HIS104 4.1 25.9 1.0
CB C:ASP63 4.1 25.6 1.0
NE2 C:GLN61 4.3 29.9 1.0
CG C:GLU100 4.3 28.1 1.0
N C:ASP63 4.3 26.3 1.0
CB C:GLU62 4.5 25.4 1.0
CD2 C:HIS103 4.6 23.4 1.0
CA C:GLU100 4.6 26.7 1.0
O C:HOH253 4.7 28.2 1.0
CA C:ASP63 4.7 26.7 1.0
CG C:GLN61 4.8 30.6 1.0
CB C:GLU100 4.8 27.0 1.0
CB C:HIS103 4.9 23.1 1.0
O C:HOH263 4.9 31.8 1.0
O C:GLU100 5.0 25.6 1.0
CG C:HIS103 5.0 21.7 1.0
O C:HOH389 5.0 36.0 1.0

Reference:

G.Prehna, C.E.Stebbins. A RAC1-Gdp Trimer Complex Binds Zinc with Tetrahedral and Octahedral Coordination, Displacing Magnesium. Acta Crystallogr.,Sect.D V. 63 628 2007.
ISSN: ISSN 0907-4449
PubMed: 17452788
DOI: 10.1107/S0907444907010888
Page generated: Thu Oct 17 02:55:30 2024

Last articles

Zn in 9J0N
Zn in 9J0O
Zn in 9J0P
Zn in 9FJX
Zn in 9EKB
Zn in 9C0F
Zn in 9CAH
Zn in 9CH0
Zn in 9CH3
Zn in 9CH1
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy